Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xdc Working: n-0-139.cluster.ucsf.bkslab.org:/scratch/xiaobo/23902/xdc-8058088.81 Result: /scratch/xiaobo/23902/xdc-8058088.81 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdc 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/xdc mkdir: created directory `/scratch/xiaobo/23902' mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81' /scratch/xiaobo/23902/xdc-8058088.81 /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/23902/xdc-8058088.81/working' mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/protonate' Storing results in /scratch/xiaobo/23902/xdc-8058088.81/finished Working in /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 /scratch/xiaobo/23902/xdc-8058088.81/working/protonate /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Using inputs as protomers/tautomers. No processing done 453 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/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Bulk generating 3D conformations all protomers in /scratch/xiaobo/23902/xdc-8058088.81/working/3D mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/23902/xdc-8058088.81/working/protonate/xdc-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 ZINC001116672487 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building' mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001116672487 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/1 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2CO)cn1) `ZINC001116672487.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116672487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001116672487 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2CO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [22, 4, 4, 4, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 16, 4, 4, 22, 22, 22, 22, 22, 4, 11, 11, 33, 11, 11, 16, 16, 48, 4] 450 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 202 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116672487 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/finished' Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116672487 Building ZINC001116682719 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116682719 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/2 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/2' -> `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)N1CCc2nn[nH]c2C1) `ZINC001116682719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116682719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116682719 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/3 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1) `ZINC001116682719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116682719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116682719 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116682719 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 Building ZINC001116682719 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116682719 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 2) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1) `ZINC001116682719.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116682719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116682719 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 3) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1) `ZINC001116682719.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116682719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116682719 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2nn[nH]c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 8, 6, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23] 32 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116682719 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116682719 Building ZINC001116696270 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696270 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/4 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696270 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 14, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 26, 26, 26, 26, 78] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/5 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696270 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 12, 2, 15, 1, 1, 1, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 24, 24, 24, 24, 72] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696270 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 Building ZINC001116696270 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696270 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 4) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696270 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 14, 2, 17, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 26, 26, 26, 26, 78] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 5) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696270 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 12, 2, 15, 1, 1, 1, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 24, 24, 24, 24, 72] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696270 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696270 Building ZINC001116696271 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696271 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/6 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696271 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 14, 2, 14, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 26, 26, 26, 26, 78] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/7 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696271 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 72] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696271 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 Building ZINC001116696271 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696271 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 6) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696271 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 14, 2, 14, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 26, 26, 26, 26, 78] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 7) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696271 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 72] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696271 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696271 Building ZINC001116696272 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696272 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/8 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696272 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 10, 2, 11, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 23, 23, 23, 23, 69] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/9 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696272 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 11, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 29, 29, 29, 29, 87] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696272 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 Building ZINC001116696272 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696272 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 8) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696272 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 10, 2, 11, 1, 1, 1, 8, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 23, 23, 23, 23, 69] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 9) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O) `ZINC001116696272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696272 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 11, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 8, 8, 8, 8, 8, 29, 29, 29, 29, 87] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696272 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696272 Building ZINC001116696273 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696273 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/10 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696273 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 72] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/11 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/11' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696273 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 14, 2, 14, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 75] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696273 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 Building ZINC001116696273 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116696273 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 10) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116696273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696273 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 13, 2, 13, 1, 1, 1, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 24, 24, 24, 24, 72] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 11) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O) `ZINC001116696273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116696273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116696273 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC[C@@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 14, 2, 14, 1, 1, 1, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 25, 25, 25, 25, 75] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116696273 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116696273 Building ZINC001116716875 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716875 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/12 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)N(C[C@H](C)O)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116716875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716875 none C[C@H](CO)N(C[C@H](C)O)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 5, 7, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 19, 4, 5, 11, 21, 21, 21, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 19, 19, 57, 11, 11, 21, 21, 21, 63, 5, 5, 5, 5, 5] 450 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/13 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)N(C[C@H](C)O)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116716875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716875 none C[C@H](CO)N(C[C@H](C)O)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 5, 7, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 13, 20, 4, 7, 14, 21, 21, 21, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 20, 20, 60, 14, 14, 21, 21, 21, 63, 5, 5, 5, 5, 5] 450 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716875 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 Building ZINC001116716875 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716875 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 12) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H](CO)N(C[C@H](C)O)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116716875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716875 none C[C@H](CO)N(C[C@H](C)O)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 5, 7, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 14, 19, 4, 5, 11, 21, 21, 21, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 14, 19, 19, 57, 11, 11, 21, 21, 21, 63, 5, 5, 5, 5, 5] 450 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 13) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H](CO)N(C[C@H](C)O)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116716875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716875 none C[C@H](CO)N(C[C@H](C)O)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 5, 7, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 13, 13, 20, 4, 7, 14, 21, 21, 21, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 13, 13, 13, 20, 20, 60, 14, 14, 21, 21, 21, 63, 5, 5, 5, 5, 5] 450 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 282 number of broken/clashed sets: 153 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716875 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716875 Building ZINC001116716876 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716876 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/14 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716876 none C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 16, 16, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 17, 16, 16, 16, 48, 13, 13, 6, 6, 6, 6, 6, 10, 10, 10, 17, 17, 51] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 224 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/15 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716876 none C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [21, 16, 21, 21, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 18, 21, 21, 21, 63, 16, 16, 6, 6, 6, 6, 6, 10, 10, 10, 18, 18, 54] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 181 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716876 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 Building ZINC001116716876 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716876 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 14) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716876.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716876 none C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [16, 13, 16, 16, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 17, 16, 16, 16, 48, 13, 13, 6, 6, 6, 6, 6, 10, 10, 10, 17, 17, 51] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 224 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 15) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716876.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716876 none C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [21, 16, 21, 21, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 18, 21, 21, 21, 63, 16, 16, 6, 6, 6, 6, 6, 10, 10, 10, 18, 18, 54] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 181 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716876 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716876 Building ZINC001116716877 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716877 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/16 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716877 none C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 22, 22, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 8, 8, 8, 18, 22, 22, 22, 66, 15, 15, 6, 6, 6, 6, 6, 8, 8, 8, 18, 18, 54] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 279 number of broken/clashed sets: 218 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/17 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716877 none C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 19, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 20, 19, 19, 19, 57, 13, 13, 6, 6, 6, 6, 6, 10, 10, 10, 20, 20, 60] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716877 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 Building ZINC001116716877 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716877 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 16) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716877 none C[C@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 22, 22, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 8, 8, 8, 18, 22, 22, 22, 66, 15, 15, 6, 6, 6, 6, 6, 8, 8, 8, 18, 18, 54] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 279 number of broken/clashed sets: 218 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 17) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO) `ZINC001116716877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716877 none C[C@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 19, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 20, 19, 19, 19, 57, 13, 13, 6, 6, 6, 6, 6, 10, 10, 10, 20, 20, 60] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716877 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716877 Building ZINC001116716878 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716878 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/18 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO) `ZINC001116716878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716878 none C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 19, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 20, 19, 19, 19, 57, 13, 13, 6, 6, 6, 6, 6, 10, 10, 10, 20, 20, 60] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/19 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO) `ZINC001116716878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716878 none C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 21, 21, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 9, 9, 9, 21, 21, 21, 21, 63, 15, 15, 6, 6, 6, 6, 6, 9, 9, 9, 21, 21, 63] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 215 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716878 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 Building ZINC001116716878 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116716878 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 18) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO) `ZINC001116716878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116716878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716878 none C[C@@H](O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 19, 19, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 20, 19, 19, 19, 57, 13, 13, 6, 6, 6, 6, 6, 10, 10, 10, 20, 20, 60] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 266 number of broken/clashed sets: 170 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 19) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO) `ZINC001116716878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116716878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001116716878 none C[C@@H](O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 4, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [21, 15, 21, 21, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 5, 9, 9, 9, 21, 21, 21, 21, 63, 15, 15, 6, 6, 6, 6, 6, 9, 9, 9, 21, 21, 63] 450 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 215 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116716878 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116716878 Building ZINC001116742670 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116742670 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/20 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1) `ZINC001116742670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116742670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742670 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 23, 11, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 4, 23, 23, 69, 24, 24, 24, 24, 24, 24, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 229 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/21 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1) `ZINC001116742670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116742670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742670 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 25, 12, 26, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 4, 25, 25, 75, 26, 26, 27, 27, 27, 27, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116742670 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 Building ZINC001116742670 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116742670 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 20) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1) `ZINC001116742670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116742670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742670 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 23, 11, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 4, 23, 23, 69, 24, 24, 24, 24, 24, 24, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 229 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 21) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1) `ZINC001116742670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116742670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742670 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 25, 12, 26, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 4, 25, 25, 75, 26, 26, 27, 27, 27, 27, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116742670 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742670 Building ZINC001116742671 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116742671 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/22 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1) `ZINC001116742671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116742671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742671 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 26, 12, 26, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 4, 26, 26, 78, 26, 26, 28, 28, 28, 28, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 262 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/23 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1) `ZINC001116742671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116742671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742671 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 23, 11, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 4, 23, 23, 69, 23, 23, 23, 23, 23, 23, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 229 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116742671 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 Building ZINC001116742671 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116742671 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 22) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1) `ZINC001116742671.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116742671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742671 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 12, 12, 26, 12, 26, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 4, 26, 26, 78, 26, 26, 28, 28, 28, 28, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 262 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 23) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1) `ZINC001116742671.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116742671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116742671 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 11, 11, 23, 11, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 4, 23, 23, 69, 23, 23, 23, 23, 23, 23, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 229 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116742671 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116742671 Building ZINC001116745975 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116745975 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/24 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1) `ZINC001116745975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116745975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116745975 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 7, 10, 37, 37, 37, 37, 37, 10, 10, 10, 8, 8, 8, 8, 8, 8, 4, 37, 10, 10, 10, 10, 10, 10, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/25 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1) `ZINC001116745975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116745975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116745975 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 12, 39, 39, 39, 39, 39, 12, 12, 12, 9, 9, 9, 9, 9, 9, 4, 39, 12, 12, 12, 12, 12, 12, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116745975 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 Building ZINC001116745975 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116745975 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 24) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1) `ZINC001116745975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116745975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116745975 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 7, 10, 37, 37, 37, 37, 37, 10, 10, 10, 8, 8, 8, 8, 8, 8, 4, 37, 10, 10, 10, 10, 10, 10, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 25) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1) `ZINC001116745975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116745975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116745975 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(c3nc[nH]n3)CCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 7, 12, 39, 39, 39, 39, 39, 12, 12, 12, 9, 9, 9, 9, 9, 9, 4, 39, 12, 12, 12, 12, 12, 12, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116745975 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116745975 Building ZINC001116747414 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116747414 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/26 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1) `ZINC001116747414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116747414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747414 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 12, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 12, 12, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/27 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1) `ZINC001116747414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116747414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747414 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 15, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 15, 15, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116747414 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 Building ZINC001116747414 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116747414 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 26) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1) `ZINC001116747414.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116747414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747414 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 12, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 12, 12, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 27) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1) `ZINC001116747414.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116747414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747414 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 3, 5, 15, 15, 15, 15, 15, 32, 32, 32, 32, 32, 15, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 32, 32, 32, 32, 32, 32, 15, 15, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116747414 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747414 Building ZINC001116747415 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116747415 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/28 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1) `ZINC001116747415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116747415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747415 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 4, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/29 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1) `ZINC001116747415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116747415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747415 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 6, 14, 14, 14, 14, 14, 34, 34, 34, 34, 34, 14, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 34, 34, 34, 34, 34, 34, 14, 14, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116747415 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 Building ZINC001116747415 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116747415 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 28) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1) `ZINC001116747415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116747415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747415 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 4, 14, 14, 14, 14, 14, 29, 29, 29, 29, 29, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 29, 29, 29, 29, 29, 29, 14, 14, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 29) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1) `ZINC001116747415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116747415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116747415 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 5, 5, 5, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 6, 14, 14, 14, 14, 14, 34, 34, 34, 34, 34, 14, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 34, 34, 34, 34, 34, 34, 14, 14, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116747415 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116747415 Building ZINC001116759936 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116759936 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/30 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1) `ZINC001116759936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116759936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116759936 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 5, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 14, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 3, 10, 10, 14, 14, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/31 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1) `ZINC001116759936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116759936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116759936 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 5, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 14, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 3, 10, 10, 14, 14, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116759936 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 Building ZINC001116759936 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116759936 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 30) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1) `ZINC001116759936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116759936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116759936 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 5, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 14, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 3, 10, 10, 14, 14, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 31) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1) `ZINC001116759936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116759936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001116759936 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(C)n2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 5, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 14, 17, 17, 17, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 3, 10, 10, 14, 14, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116759936 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116759936 Building ZINC001116770029 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116770029 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/32 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116770029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770029 none C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10] 42 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/33 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116770029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770029 none C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116770029 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 Building ZINC001116770029 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116770029 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 32) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116770029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770029 none C[C@@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10] 42 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 33) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116770029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770029 none C[C@@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116770029 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770029 Building ZINC001116770030 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116770030 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/34 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116770030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770030 none C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/35 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116770030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770030 none C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10] 42 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116770030 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 Building ZINC001116770030 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116770030 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 34) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116770030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770030 none C[C@H]1c2nncn2CCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 35) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001116770030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116770030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001116770030 none C[C@H]1c2nncn2CCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10] 42 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 43 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116770030 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116770030 Building ZINC001116883915 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116883915 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/36 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1) `ZINC001116883915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116883915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883915 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 7, 17, 27, 28, 28, 2, 2, 3, 3, 3, 3, 3, 2, 2, 10, 10, 30, 17, 17, 28, 28, 28, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/37 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1) `ZINC001116883915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116883915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883915 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 9, 6, 13, 24, 24, 24, 3, 3, 8, 8, 8, 8, 8, 3, 2, 9, 9, 27, 13, 13, 24, 24, 24, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116883915 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 Building ZINC001116883915 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116883915 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 36) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1) `ZINC001116883915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116883915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883915 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 10, 7, 17, 27, 28, 28, 2, 2, 3, 3, 3, 3, 3, 2, 2, 10, 10, 30, 17, 17, 28, 28, 28, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 37) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1) `ZINC001116883915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116883915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883915 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 9, 6, 13, 24, 24, 24, 3, 3, 8, 8, 8, 8, 8, 3, 2, 9, 9, 27, 13, 13, 24, 24, 24, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116883915 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883915 Building ZINC001116883916 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116883916 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/38 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1) `ZINC001116883916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116883916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883916 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 9, 6, 13, 24, 24, 24, 3, 3, 8, 8, 8, 8, 8, 3, 2, 9, 9, 27, 13, 13, 24, 24, 24, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/39 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1) `ZINC001116883916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116883916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883916 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 9, 6, 16, 27, 28, 28, 2, 2, 5, 5, 5, 5, 5, 2, 2, 9, 9, 27, 16, 16, 28, 28, 28, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116883916 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 Building ZINC001116883916 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116883916 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 38) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1) `ZINC001116883916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116883916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883916 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 9, 6, 13, 24, 24, 24, 3, 3, 8, 8, 8, 8, 8, 3, 2, 9, 9, 27, 13, 13, 24, 24, 24, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 39) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1) `ZINC001116883916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116883916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001116883916 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC(C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 1, 5, 11, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 9, 6, 16, 27, 28, 28, 2, 2, 5, 5, 5, 5, 5, 2, 2, 9, 9, 27, 16, 16, 28, 28, 28, 2] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116883916 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116883916 Building ZINC001116891674 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891674 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/40 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1) `ZINC001116891674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891674 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 7, 16, 18, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 36, 16, 16, 18, 18, 18, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/41 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1) `ZINC001116891674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891674 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 14, 8, 18, 19, 5, 5, 12, 12, 12, 12, 12, 5, 2, 14, 14, 42, 18, 18, 19, 19, 19, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891674 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 Building ZINC001116891674 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891674 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 40) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1) `ZINC001116891674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891674 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 7, 16, 18, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 36, 16, 16, 18, 18, 18, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 170 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 41) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1) `ZINC001116891674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891674 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 14, 8, 18, 19, 5, 5, 12, 12, 12, 12, 12, 5, 2, 14, 14, 42, 18, 18, 19, 19, 19, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891674 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891674 Building ZINC001116891675 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891675 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/42 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1) `ZINC001116891675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891675 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 7, 18, 20, 5, 5, 12, 12, 12, 12, 12, 5, 2, 13, 13, 39, 18, 18, 20, 20, 20, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/43 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1) `ZINC001116891675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891675 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 7, 16, 17, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 36, 16, 16, 17, 17, 17, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891675 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 Building ZINC001116891675 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891675 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 42) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1) `ZINC001116891675.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891675 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 13, 7, 18, 20, 5, 5, 12, 12, 12, 12, 12, 5, 2, 13, 13, 39, 18, 18, 20, 20, 20, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 191 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 43) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1) `ZINC001116891675.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891675 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)COC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 7, 16, 17, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 36, 16, 16, 17, 17, 17, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891675 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891675 Building ZINC001116891746 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891746 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/44 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1) `ZINC001116891746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891746 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 32, 32, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 32, 32, 15, 15, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/45 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1) `ZINC001116891746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891746 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 4, 14, 14, 14, 14, 14, 28, 28, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 28, 28, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891746 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 Building ZINC001116891746 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891746 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 44) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1) `ZINC001116891746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891746 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 32, 32, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 32, 32, 15, 15, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 45) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1) `ZINC001116891746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891746 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 4, 14, 14, 14, 14, 14, 28, 28, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 28, 28, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891746 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891746 Building ZINC001116891747 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891747 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/46 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1) `ZINC001116891747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891747 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 13, 28, 28, 13, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 28, 28, 13, 13, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/47 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1) `ZINC001116891747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891747 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 14, 34, 34, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 34, 34, 14, 14, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891747 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 Building ZINC001116891747 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116891747 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 46) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1) `ZINC001116891747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116891747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891747 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 13, 28, 28, 13, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 28, 28, 13, 13, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 47) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1) `ZINC001116891747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116891747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116891747 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(N)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 14, 34, 34, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 34, 34, 14, 14, 5] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116891747 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116891747 Building ZINC001116892900 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116892900 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/48 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1) `ZINC001116892900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116892900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001116892900 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 8, 6, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 14, 26, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 2, 11, 11, 17, 17, 24, 25, 46, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/49 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1) `ZINC001116892900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116892900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001116892900 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 8, 6, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 14, 27, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 2, 13, 13, 18, 18, 25, 25, 48, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116892900 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 Building ZINC001116892900 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116892900 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 48) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1) `ZINC001116892900.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116892900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001116892900 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 8, 6, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 14, 26, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 2, 11, 11, 17, 17, 24, 25, 46, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 49) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1) `ZINC001116892900.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116892900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001116892900 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nc[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 1, 8, 6, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 14, 27, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 2, 13, 13, 18, 18, 25, 25, 48, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116892900 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116892900 Building ZINC001116907273 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116907273 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/50 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1) `ZINC001116907273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116907273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116907273 none CCn1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 8, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 12, 12, 9, 25, 25, 25, 25, 25, 9, 4, 8, 8, 8, 8, 8, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/51 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1) `ZINC001116907273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116907273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116907273 none CCn1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 8, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 13, 13, 9, 25, 25, 25, 25, 25, 9, 4, 8, 8, 8, 8, 8, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116907273 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 Building ZINC001116907273 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001116907273 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 50) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1) `ZINC001116907273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001116907273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116907273 none CCn1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 8, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 12, 12, 9, 25, 25, 25, 25, 25, 9, 4, 8, 8, 8, 8, 8, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 51) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1) `ZINC001116907273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001116907273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001116907273 none CCn1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)c(C(N)=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 8, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 9, 9, 13, 13, 9, 25, 25, 25, 25, 25, 9, 4, 8, 8, 8, 8, 8, 13, 13] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001116907273 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001116907273 Building ZINC001117131683 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117131683 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/52 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1) `ZINC001117131683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117131683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117131683 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 18, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 150, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/53 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1) `ZINC001117131683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117131683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117131683 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 17, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 17, 17, 150, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 305 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117131683 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 Building ZINC001117131683 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117131683 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 52) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1) `ZINC001117131683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117131683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117131683 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 18, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 18, 18, 150, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 53) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1) `ZINC001117131683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117131683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117131683 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1(O)CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 4, 4, 17, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 17, 17, 150, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 305 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117131683 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117131683 Building ZINC001117378373 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117378373 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/54 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1) `ZINC001117378373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117378373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378373 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/55 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1) `ZINC001117378373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117378373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378373 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 35, 35, 35, 35, 35, 35, 35, 13, 13, 13, 6, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117378373 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 Building ZINC001117378373 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117378373 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 54) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1) `ZINC001117378373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117378373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378373 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 11, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 55) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1) `ZINC001117378373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117378373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378373 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 35, 35, 35, 35, 35, 35, 35, 13, 13, 13, 6, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 95 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117378373 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378373 Building ZINC001117378374 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117378374 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/56 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1) `ZINC001117378374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117378374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378374 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 13, 36, 36, 36, 36, 36, 36, 36, 13, 13, 13, 7, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/57 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1) `ZINC001117378374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117378374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378374 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 10, 33, 33, 33, 33, 33, 33, 33, 9, 9, 9, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 90 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117378374 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 Building ZINC001117378374 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117378374 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 56) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1) `ZINC001117378374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117378374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378374 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 13, 36, 36, 36, 36, 36, 36, 36, 13, 13, 13, 7, 7, 7, 7, 7, 7, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 98 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 57) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1) `ZINC001117378374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117378374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117378374 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCS(=O)(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 14, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 10, 33, 33, 33, 33, 33, 33, 33, 9, 9, 9, 6, 6, 6, 6, 6, 6, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 90 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117378374 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117378374 Building ZINC001117388265 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117388265 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/58 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1) `ZINC001117388265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117388265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117388265 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 41, 48, 48, 14, 5, 5, 5, 5, 5, 5, 3, 14, 41, 41, 48, 48, 14] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/59 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1) `ZINC001117388265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117388265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117388265 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 42, 47, 47, 14, 5, 5, 5, 5, 5, 5, 3, 14, 42, 42, 47, 47, 14] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117388265 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 Building ZINC001117388265 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117388265 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 58) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1) `ZINC001117388265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117388265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117388265 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 41, 48, 48, 14, 5, 5, 5, 5, 5, 5, 3, 14, 41, 41, 48, 48, 14] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 59) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1) `ZINC001117388265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117388265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117388265 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1cnn(CC(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 42, 47, 47, 14, 5, 5, 5, 5, 5, 5, 3, 14, 42, 42, 47, 47, 14] 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]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117388265 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117388265 Building ZINC001117389072 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117389072 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/60 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1) `ZINC001117389072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117389072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117389072 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 32, 30, 32, 32, 8, 8, 8, 8, 8, 8, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/61 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1) `ZINC001117389072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117389072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117389072 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 31, 31, 31, 31, 29, 31, 31, 8, 8, 8, 8, 8, 8, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31] 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]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117389072 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 Building ZINC001117389072 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117389072 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 60) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1) `ZINC001117389072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117389072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117389072 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 32, 30, 32, 32, 8, 8, 8, 8, 8, 8, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 61) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1) `ZINC001117389072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117389072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001117389072 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 31, 31, 31, 31, 29, 31, 31, 8, 8, 8, 8, 8, 8, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31] 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]) total number of confs: 87 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117389072 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117389072 Building ZINC001117402939 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001117402939 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/62 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/63 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/64 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/64' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/65 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/65' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117402939 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 Building ZINC001117402939 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001117402939 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 62) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 63) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 64) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 65) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117402939 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 Building ZINC001117402939 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001117402939 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 62) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 63) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 64) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 65) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117402939 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 Building ZINC001117402939 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001117402939 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 62) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 63) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 64) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 35, 49, 22, 17, 22, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 49, 49, 49, 35, 35, 22, 22, 22, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 65) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001117402939.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001117402939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001117402939 none COC(=O)CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 24, 17, 24, 13, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 50, 50, 50, 37, 37, 24, 24, 24, 17, 17, 13, 13, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117402939 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117402939 Building ZINC001117419916 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117419916 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/66 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1) `ZINC001117419916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117419916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117419916 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 17, 41, 44, 44, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 41, 41, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/67 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1) `ZINC001117419916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117419916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117419916 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 16, 39, 42, 42, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 39, 39, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117419916 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 Building ZINC001117419916 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117419916 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 66) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1) `ZINC001117419916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117419916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117419916 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 17, 41, 44, 44, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 41, 41, 44, 44, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 67) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1) `ZINC001117419916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117419916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001117419916 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(OCC(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 16, 39, 42, 42, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 39, 39, 42, 42, 6, 6, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117419916 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117419916 Building ZINC001117439190 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117439190 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/68 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1) `ZINC001117439190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117439190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117439190 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 43, 43, 43, 47, 47, 43, 43, 4, 4, 4, 4, 4, 4, 3, 17, 17, 43, 47, 47] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/69 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1) `ZINC001117439190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117439190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117439190 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 43, 43, 43, 47, 47, 43, 43, 4, 4, 4, 4, 4, 4, 3, 17, 17, 43, 47, 47] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117439190 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 Building ZINC001117439190 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117439190 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 68) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1) `ZINC001117439190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117439190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117439190 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 43, 43, 43, 47, 47, 43, 43, 4, 4, 4, 4, 4, 4, 3, 17, 17, 43, 47, 47] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 69) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1) `ZINC001117439190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117439190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117439190 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCc1cc(C(N)=O)no1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 17, 43, 43, 43, 47, 47, 43, 43, 4, 4, 4, 4, 4, 4, 3, 17, 17, 43, 47, 47] 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117439190 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117439190 Building ZINC001117447467 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117447467 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/70 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117447467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447467 none COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 31, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 18, 18, 43, 43, 43, 31, 31, 23, 23, 4, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/71 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117447467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447467 none COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 29, 21, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 15, 15, 39, 39, 39, 29, 29, 21, 21, 4, 5, 5, 5, 5, 5, 5, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117447467 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 Building ZINC001117447467 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117447467 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 70) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447467.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117447467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447467 none COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 31, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 18, 18, 43, 43, 43, 31, 31, 23, 23, 4, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 71) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447467.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117447467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447467 none COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 29, 21, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 15, 15, 39, 39, 39, 29, 29, 21, 21, 4, 5, 5, 5, 5, 5, 5, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117447467 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447467 Building ZINC001117447469 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117447469 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/72 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117447469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447469 none COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 29, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 18, 18, 39, 39, 39, 29, 29, 23, 23, 4, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/73 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117447469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447469 none COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 31, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 18, 18, 43, 43, 43, 31, 31, 23, 23, 4, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117447469 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 Building ZINC001117447469 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117447469 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 72) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117447469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447469 none COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 29, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 18, 18, 39, 39, 39, 29, 29, 23, 23, 4, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 73) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O) `ZINC001117447469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117447469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117447469 none COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 31, 23, 8, 4, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 18, 18, 43, 43, 43, 31, 31, 23, 23, 4, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117447469 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117447469 Building ZINC001117477022 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117477022 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/74 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](CCSC)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117477022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117477022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117477022 none CNC(=O)[C@H](CCSC)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 8, 2, 5, 5, 13, 15, 38, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 15, 15, 15, 15, 38, 38, 38, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/75 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](CCSC)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117477022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117477022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117477022 none CNC(=O)[C@H](CCSC)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 14, 15, 33, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 33, 33, 33, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117477022 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 Building ZINC001117477022 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117477022 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 74) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CNC(=O)[C@H](CCSC)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117477022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117477022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117477022 none CNC(=O)[C@H](CCSC)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 5, 8, 2, 5, 5, 13, 15, 38, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 8, 15, 15, 15, 15, 38, 38, 38, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 75) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CNC(=O)[C@H](CCSC)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117477022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117477022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117477022 none CNC(=O)[C@H](CCSC)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'S.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 14, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 14, 15, 33, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 33, 33, 33, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117477022 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117477022 Building ZINC001117523159 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117523159 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/76 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1) `ZINC001117523159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117523159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117523159 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 10, 10, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/77 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/77' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1) `ZINC001117523159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117523159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117523159 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 17, 17, 6, 6, 17, 17, 17, 17, 17, 6, 2, 10, 10, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117523159 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 Building ZINC001117523159 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117523159 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 76) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1) `ZINC001117523159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117523159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117523159 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 6, 6, 17, 17, 17, 17, 17, 6, 2, 10, 10, 16, 16, 16, 16, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 77) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1) `ZINC001117523159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117523159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117523159 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 17, 17, 17, 6, 6, 17, 17, 17, 17, 17, 6, 2, 10, 10, 17, 17, 17, 17, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117523159 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117523159 Building ZINC001117665447 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117665447 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/78 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1) `ZINC001117665447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117665447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117665447 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 2, 11, 16, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30] 42 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/79 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1) `ZINC001117665447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117665447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117665447 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 2, 9, 14, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21] 32 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117665447 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 Building ZINC001117665447 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117665447 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 78) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1) `ZINC001117665447.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117665447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117665447 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 2, 11, 16, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30] 42 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 79) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1) `ZINC001117665447.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117665447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117665447 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 2, 9, 14, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21] 32 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117665447 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117665447 Building ZINC001117669059 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117669059 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/80 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1) `ZINC001117669059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117669059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117669059 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 23, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 14, 14, 23, 23, 48, 48] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/81 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1) `ZINC001117669059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117669059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117669059 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 23, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 14, 14, 23, 23, 48, 48] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117669059 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 Building ZINC001117669059 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117669059 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 80) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1) `ZINC001117669059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117669059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117669059 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 23, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 14, 14, 23, 23, 48, 48] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 81) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1) `ZINC001117669059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117669059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117669059 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCc1nnc(N)o1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 14, 23, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 14, 14, 23, 23, 48, 48] 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]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117669059 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669059 Building ZINC001117669306 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117669306 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/82 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n1) `ZINC001117669306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117669306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117669306 none Cn1cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 40, 40, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 40, 40, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 85 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/83 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1) `ZINC001117669306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117669306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117669306 none Cn1cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 39, 39, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 39, 39, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117669306 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 Building ZINC001117669306 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117669306 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 82) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n1) `ZINC001117669306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117669306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117669306 none Cn1cc(C(N)=O)c(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 40, 40, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 40, 40, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 85 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 83) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1) `ZINC001117669306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117669306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117669306 none Cn1cc(C(N)=O)c(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 39, 39, 5, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 39, 39, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117669306 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117669306 Building ZINC001117672567 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117672567 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/84 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO) `ZINC001117672567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117672567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117672567 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 36, 7, 7, 7, 7, 7, 7, 19, 19, 57, 19, 19, 36, 36, 108] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 288 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/85 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO) `ZINC001117672567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117672567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117672567 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 40, 7, 7, 7, 7, 7, 7, 18, 18, 54, 18, 18, 40, 40, 120] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 317 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117672567 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 Building ZINC001117672567 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117672567 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 84) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO) `ZINC001117672567.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117672567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117672567 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 19, 36, 7, 7, 7, 7, 7, 7, 19, 19, 57, 19, 19, 36, 36, 108] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 288 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 85) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO) `ZINC001117672567.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117672567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117672567 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@H](O)C[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 10, 10, 18, 18, 18, 18, 18, 18, 18, 18, 40, 7, 7, 7, 7, 7, 7, 18, 18, 54, 18, 18, 40, 40, 120] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 317 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117672567 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117672567 Building ZINC001117683371 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117683371 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/86 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117683371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117683371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117683371 none COCCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 37, 19, 8, 6, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 40, 39, 39, 37, 37, 8, 8, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/87 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117683371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117683371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117683371 none COCCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 37, 19, 8, 6, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 40, 39, 39, 37, 37, 8, 8, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117683371 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 Building ZINC001117683371 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117683371 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 86) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COCCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117683371.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117683371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117683371 none COCCOCCN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 37, 19, 8, 6, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 40, 39, 39, 37, 37, 8, 8, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 87) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: COCCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001117683371.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117683371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001117683371 none COCCOCCN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 39, 37, 19, 8, 6, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 40, 40, 40, 39, 39, 37, 37, 8, 8, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [7, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117683371 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117683371 Building ZINC001117707104 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117707104 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/88 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n[nH]1) `ZINC001117707104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117707104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117707104 none COC(=O)Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 21, 43, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 43, 43, 43, 21, 21, 3, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/89 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n[nH]1) `ZINC001117707104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117707104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117707104 none COC(=O)Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 21, 44, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 44, 44, 44, 21, 21, 3, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117707104 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 Building ZINC001117707104 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117707104 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 88) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n[nH]1) `ZINC001117707104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117707104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117707104 none COC(=O)Cc1nc(NC(=O)[C@]([O-])([SiH3])c2cccn2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 21, 43, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 43, 43, 43, 21, 21, 3, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 89) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n[nH]1) `ZINC001117707104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117707104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001117707104 none COC(=O)Cc1nc(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 21, 44, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 4, 4, 4, 44, 44, 44, 21, 21, 3, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117707104 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117707104 Building ZINC001117738157 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117738157 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/90 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1) `ZINC001117738157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117738157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117738157 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 14, 28, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4, 18, 18, 21, 21, 24, 26, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/91 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1) `ZINC001117738157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117738157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117738157 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 14, 28, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 4, 18, 18, 21, 21, 26, 24, 33, 33, 33, 33, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117738157 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 Building ZINC001117738157 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117738157 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 90) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1) `ZINC001117738157.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117738157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117738157 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 14, 28, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 4, 18, 18, 21, 21, 24, 26, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 91) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1) `ZINC001117738157.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117738157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001117738157 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCCc2nncn2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 1, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 14, 28, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 4, 18, 18, 21, 21, 26, 24, 33, 33, 33, 33, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117738157 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117738157 Building ZINC001117763006 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117763006 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/92 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1) `ZINC001117763006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117763006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117763006 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/93 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1) `ZINC001117763006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117763006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117763006 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117763006 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 Building ZINC001117763006 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117763006 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 92) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1) `ZINC001117763006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117763006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117763006 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 93) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1) `ZINC001117763006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117763006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001117763006 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3nc[nH]c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 6, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117763006 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117763006 Building ZINC001117767478 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117767478 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/94 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117767478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767478 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2] 5 rigid atoms, others: [3, 4, 5, 6, 7] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/95 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117767478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767478 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 11, 18, 18, 18, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 11, 11, 18, 18, 18, 7, 7, 5] 34 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117767478 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 Building ZINC001117767478 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117767478 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 94) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117767478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767478 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2] 5 rigid atoms, others: [3, 4, 5, 6, 7] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 95) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117767478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767478 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 11, 18, 18, 18, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 11, 11, 18, 18, 18, 7, 7, 5] 34 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117767478 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767478 Building ZINC001117767479 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117767479 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/96 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117767479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767479 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 11, 20, 20, 20, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 11, 11, 20, 20, 20, 7, 7, 5] 30 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/97 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117767479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767479 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2] 5 rigid atoms, others: [3, 4, 5, 6, 7] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117767479 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 Building ZINC001117767479 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117767479 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 96) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117767479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767479 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 7, 11, 20, 20, 20, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 11, 11, 20, 20, 20, 7, 7, 5] 30 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 97) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1) `ZINC001117767479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117767479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001117767479 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](CS(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2] 5 rigid atoms, others: [3, 4, 5, 6, 7] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117767479 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117767479 Building ZINC001117775407 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117775407 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/98 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/98' -> `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)Nc1nnc2nc[nH]n21) `ZINC001117775407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117775407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117775407 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/99 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21) `ZINC001117775407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117775407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117775407 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117775407 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 Building ZINC001117775407 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117775407 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 98) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21) `ZINC001117775407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117775407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117775407 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 99) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21) `ZINC001117775407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117775407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117775407 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc2nc[nH]n21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 8, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 15] 18 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117775407 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117775407 Building ZINC001117780523 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117780523 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/100 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc[nH]n1) `ZINC001117780523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117780523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117780523 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 17, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 17, 17, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/101 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc[nH]n1) `ZINC001117780523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117780523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117780523 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 18, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117780523 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 Building ZINC001117780523 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001117780523 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 100) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc[nH]n1) `ZINC001117780523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001117780523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117780523 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 17, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 17, 17, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 101) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc[nH]n1) `ZINC001117780523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001117780523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001117780523 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 18, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 18, 18, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001117780523 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001117780523 Building ZINC001118006884 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118006884 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/102 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1) `ZINC001118006884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006884 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 19, 19, 19, 8, 5, 5, 18, 18, 18, 18, 18, 5, 8, 8, 8, 8, 19, 19, 19, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/103 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1) `ZINC001118006884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006884 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 8, 4, 4, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 21, 21, 21, 8, 8, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118006884 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 Building ZINC001118006884 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118006884 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 102) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1) `ZINC001118006884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006884 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 2, 3, 8, 8, 8, 8, 8, 19, 19, 19, 8, 5, 5, 18, 18, 18, 18, 18, 5, 8, 8, 8, 8, 19, 19, 19, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 103) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1) `ZINC001118006884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118006884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006884 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 8, 4, 4, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 21, 21, 21, 8, 8, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118006884 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006884 Building ZINC001118006885 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118006885 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/104 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1) `ZINC001118006885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118006885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006885 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 8, 4, 4, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 21, 21, 21, 8, 8, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/105 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1) `ZINC001118006885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118006885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006885 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 19, 19, 19, 9, 5, 5, 16, 16, 16, 16, 16, 5, 9, 9, 9, 9, 19, 19, 19, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118006885 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 Building ZINC001118006885 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118006885 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 104) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1) `ZINC001118006885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118006885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006885 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 8, 4, 4, 14, 14, 14, 14, 14, 4, 8, 8, 8, 8, 21, 21, 21, 8, 8, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 105) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1) `ZINC001118006885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118006885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118006885 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](S(C)(=O)=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 14, 5, 11, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 1, 2, 3, 9, 9, 9, 9, 9, 19, 19, 19, 9, 5, 5, 16, 16, 16, 16, 16, 5, 9, 9, 9, 9, 19, 19, 19, 9, 9, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118006885 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118006885 Building ZINC001118140082 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140082 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/106 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140082 none C[C@@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 13, 28, 28, 13, 13, 13, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/107 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140082 none C[C@@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 27, 27, 14, 14, 14, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 27, 27, 27, 27, 27, 14, 14, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140082 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 Building ZINC001118140082 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140082 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 106) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140082 none C[C@@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 13, 28, 28, 13, 13, 13, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 107) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140082 none C[C@@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 27, 27, 14, 14, 14, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 27, 27, 27, 27, 27, 14, 14, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140082 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140082 Building ZINC001118140083 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140083 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/108 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140083 none C[C@@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 12, 31, 31, 12, 12, 12, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 31, 31, 31, 31, 31, 12, 12, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/109 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140083 none C[C@@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 10, 26, 26, 10, 10, 10, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 26, 26, 26, 26, 26, 10, 10, 5, 5, 5, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140083 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 Building ZINC001118140083 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140083 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 108) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140083 none C[C@@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 12, 31, 31, 12, 12, 12, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 31, 31, 31, 31, 31, 12, 12, 6, 6, 6, 6, 6, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 109) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140083 none C[C@@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 10, 26, 26, 10, 10, 10, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 10, 10, 10, 26, 26, 26, 26, 26, 10, 10, 5, 5, 5, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140083 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140083 Building ZINC001118140084 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140084 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/110 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140084 none C[C@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 28, 15, 15, 15, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 28, 28, 28, 28, 28, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/111 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140084 none C[C@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 29, 15, 15, 15, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 29, 29, 29, 29, 29, 15, 15, 6, 6, 6, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140084 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 Building ZINC001118140084 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140084 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 110) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140084 none C[C@H](N)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 15, 28, 28, 15, 15, 15, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 28, 28, 28, 28, 28, 15, 15, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 111) grep: /scratch/xiaobo/23902/xdc-8058088.81/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: C[C@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140084 none C[C@H](N)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 29, 15, 15, 15, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 29, 29, 29, 29, 29, 15, 15, 6, 6, 6, 6, 6, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140084 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140084 Building ZINC001118140085 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140085 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/112 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140085 none C[C@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 30, 30, 13, 13, 13, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 30, 30, 30, 30, 30, 13, 13, 7, 7, 7, 7, 7, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/113 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140085 none C[C@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 13, 27, 27, 13, 13, 13, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 27, 27, 27, 27, 27, 13, 13, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140085 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 Building ZINC001118140085 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118140085 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 112) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118140085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140085 none C[C@H](N)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 13, 30, 30, 13, 13, 13, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 13, 13, 13, 30, 30, 30, 30, 30, 13, 13, 7, 7, 7, 7, 7, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 113) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1) `ZINC001118140085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118140085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118140085 none C[C@H](N)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 13, 27, 27, 13, 13, 13, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 27, 27, 27, 27, 27, 13, 13, 6, 6, 6, 6, 6, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118140085 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118140085 Building ZINC001118261459 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118261459 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/114 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1) `ZINC001118261459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118261459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118261459 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 20, 34, 35, 35, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 4, 17, 17, 105, 34, 34, 34, 34, 34, 34, 34, 34, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/115 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1) `ZINC001118261459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118261459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118261459 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 22, 34, 37, 37, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 4, 19, 19, 111, 34, 34, 34, 34, 34, 34, 34, 34, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 240 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118261459 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 Building ZINC001118261459 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118261459 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 114) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1) `ZINC001118261459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118261459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118261459 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 20, 34, 35, 35, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 7, 4, 17, 17, 105, 34, 34, 34, 34, 34, 34, 34, 34, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 115) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1) `ZINC001118261459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118261459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118261459 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2(C(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 22, 34, 37, 37, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 4, 19, 19, 111, 34, 34, 34, 34, 34, 34, 34, 34, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 240 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118261459 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118261459 Building ZINC001118317926 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118317926 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/116 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC001118317926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118317926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118317926 none Cc1noc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 14, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 14, 14, 5, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/117 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC001118317926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118317926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118317926 none Cc1noc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 14, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 14, 14, 5, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118317926 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 Building ZINC001118317926 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118317926 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 116) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC001118317926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118317926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118317926 none Cc1noc(CN(C)C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 14, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 14, 14, 5, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 117) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC001118317926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118317926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118317926 none Cc1noc(CN(C)C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 14, 5, 2, 5, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 14, 14, 5, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118317926 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118317926 Building ZINC001118372470 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118372470 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/118 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1) `ZINC001118372470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118372470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118372470 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 14, 20, 32, 32, 32, 32, 32, 40, 32, 32, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 40, 32, 32, 32, 32] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/119 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1) `ZINC001118372470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118372470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118372470 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 13, 21, 31, 31, 31, 31, 31, 38, 31, 31, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 38, 31, 31, 31, 31] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118372470 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 Building ZINC001118372470 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118372470 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 118) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1) `ZINC001118372470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118372470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118372470 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 14, 20, 32, 32, 32, 32, 32, 40, 32, 32, 6, 6, 6, 6, 6, 6, 32, 32, 32, 32, 32, 32, 40, 32, 32, 32, 32] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 119) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1) `ZINC001118372470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118372470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118372470 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCCN(C=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 13, 21, 31, 31, 31, 31, 31, 38, 31, 31, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 38, 31, 31, 31, 31] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118372470 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118372470 Building ZINC001118390277 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118390277 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/120 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118390277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390277 none Cn1nnc2c1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 11, 27, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 6, 10, 10, 10, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/121 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118390277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390277 none Cn1nnc2c1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 12, 30, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 6, 10, 10, 10, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118390277 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 Building ZINC001118390277 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118390277 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 120) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118390277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390277 none Cn1nnc2c1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 11, 27, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 6, 10, 10, 10, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 121) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118390277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390277 none Cn1nnc2c1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 12, 30, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 6, 10, 10, 10, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118390277 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390277 Building ZINC001118390278 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118390278 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/122 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118390278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390278 none Cn1nnc2c1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 12, 30, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 6, 10, 10, 10, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/123 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118390278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390278 none Cn1nnc2c1CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 11, 27, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 6, 10, 10, 10, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118390278 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 Building ZINC001118390278 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118390278 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 122) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390278.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118390278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390278 none Cn1nnc2c1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 12, 30, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 30, 6, 10, 10, 10, 30, 30] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 123) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc2c1CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2) `ZINC001118390278.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118390278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118390278 none Cn1nnc2c1CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc[nH]1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 11, 27, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 6, 10, 10, 10, 27, 27] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118390278 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118390278 Building ZINC001118510744 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118510744 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/124 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1) `ZINC001118510744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118510744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118510744 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 16, 31, 33, 33, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 5, 31, 31, 99, 16, 16, 16, 16, 16, 16, 16, 16, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/125 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1) `ZINC001118510744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118510744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118510744 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 16, 28, 31, 31, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 9, 5, 28, 28, 93, 16, 16, 16, 16, 16, 16, 16, 16, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 217 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118510744 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 Building ZINC001118510744 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118510744 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 124) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1) `ZINC001118510744.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118510744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118510744 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 16, 31, 33, 33, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 5, 31, 31, 99, 16, 16, 16, 16, 16, 16, 16, 16, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 125) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1) `ZINC001118510744.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118510744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118510744 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2(CC(=O)O)CCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 16, 28, 31, 31, 16, 16, 16, 16, 16, 9, 9, 9, 9, 9, 9, 5, 28, 28, 93, 16, 16, 16, 16, 16, 16, 16, 16, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 217 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118510744 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118510744 Building ZINC001118517627 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118517627 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/126 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118517627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118517627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118517627 none CC(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 4, 7, 1, 4, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 5, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/127 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118517627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118517627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118517627 none CC(C)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 22, 22, 22, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 6, 22, 22, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118517627 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 Building ZINC001118517627 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118517627 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 126) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118517627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118517627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118517627 none CC(C)N(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 4, 7, 1, 4, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 5, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 127) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118517627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118517627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118517627 none CC(C)N(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 22, 22, 22, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 6, 22, 22, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118517627 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118517627 Building ZINC001118572918 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118572918 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/128 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1C) `ZINC001118572918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118572918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118572918 none Cc1c(CN)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 10, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 30, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 5, 9, 9, 9, 9, 9, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/129 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1C) `ZINC001118572918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118572918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118572918 none Cc1c(CN)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 10, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 29, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 29, 29, 29, 29, 4, 11, 11, 11, 11, 11, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118572918 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 Building ZINC001118572918 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118572918 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 128) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1C) `ZINC001118572918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118572918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118572918 none Cc1c(CN)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 10, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 30, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 30, 30, 30, 30, 5, 9, 9, 9, 9, 9, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 129) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CN)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1C) `ZINC001118572918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118572918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001118572918 none Cc1c(CN)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 10, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 29, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 29, 29, 29, 29, 4, 11, 11, 11, 11, 11, 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118572918 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118572918 Building ZINC001118579996 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118579996 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/130 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118579996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118579996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118579996 none CCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 5, 6, 1, 5, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 9, 9, 9, 9, 9, 6, 6, 6, 5, 19, 19, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/131 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118579996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118579996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118579996 none CCN(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 5, 6, 1, 5, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5, 5, 9, 9, 9, 9, 9, 6, 6, 6, 5, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118579996 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 Building ZINC001118579996 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118579996 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 130) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118579996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118579996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118579996 none CCN(C)C(=O)[C@@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 5, 6, 1, 5, 1, 1, 1, 5, 5, 5, 19, 19, 19, 5, 5, 5, 9, 9, 9, 9, 9, 6, 6, 6, 5, 19, 19, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 131) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C) `ZINC001118579996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118579996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118579996 none CCN(C)C(=O)[C@]([O-])([SiH3])c1cc(S(N)(=O)=O)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 14, 8, 11, 11, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 5, 6, 1, 5, 1, 1, 1, 5, 5, 5, 20, 20, 20, 5, 5, 5, 9, 9, 9, 9, 9, 6, 6, 6, 5, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118579996 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118579996 Building ZINC001118720064 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720064 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/132 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720064 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 2, 7, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/133 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720064 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 2, 8, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720064 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 Building ZINC001118720064 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720064 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 132) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720064 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 2, 7, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 133) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720064 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 2, 8, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720064 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720064 Building ZINC001118720066 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720066 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/134 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720066 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 8, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/135 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720066 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 2, 11, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720066 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 Building ZINC001118720066 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720066 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 134) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720066 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 8, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 135) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720066 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 2, 11, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720066 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720066 Building ZINC001118720068 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720068 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/136 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720068 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 2, 10, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/137 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720068 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 2, 10, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720068 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 Building ZINC001118720068 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720068 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 136) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720068 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 2, 10, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 137) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1) `ZINC001118720068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720068 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H]3NC(=O)CC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 2, 10, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720068 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720068 Building ZINC001118720070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/138 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720070 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 2, 10, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/139 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720070 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 2, 10, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 Building ZINC001118720070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118720070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 138) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118720070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720070 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 2, 10, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 139) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1) `ZINC001118720070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118720070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001118720070 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H]3NC(=O)CC[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 2, 10, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 7] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118720070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118720070 Building ZINC001118731270 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118731270 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/140 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(C)nn1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001118731270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118731270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118731270 none CN(Cc1cn(C)nn1)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 22, 38, 38, 38, 38, 38, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 22, 22, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/141 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001118731270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118731270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118731270 none CN(Cc1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 21, 38, 38, 38, 38, 38, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 21, 21, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118731270 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 Building ZINC001118731270 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118731270 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 140) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(C)nn1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC001118731270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118731270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118731270 none CN(Cc1cn(C)nn1)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 22, 38, 38, 38, 38, 38, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 22, 22, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 141) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC001118731270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118731270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118731270 none CN(Cc1cn(C)nn1)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 5, 8, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 21, 38, 38, 38, 38, 38, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 21, 21, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118731270 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118731270 Building ZINC001118740521 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118740521 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/142 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N1CCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118740521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118740521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118740521 none CN(CC(=O)N1CCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 27, 27, 32, 32, 32, 32, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/143 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N1CCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118740521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118740521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118740521 none CN(CC(=O)N1CCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 29, 32, 32, 32, 32, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118740521 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 Building ZINC001118740521 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118740521 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 142) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N1CCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118740521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118740521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118740521 none CN(CC(=O)N1CCCC1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 27, 27, 32, 32, 32, 32, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 143) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N1CCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118740521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118740521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001118740521 none CN(CC(=O)N1CCCC1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 29, 29, 32, 32, 32, 32, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118740521 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118740521 Building ZINC001118777913 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118777913 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/144 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1) `ZINC001118777913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118777913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118777913 none CCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 20, 20, 20, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 20, 20, 39, 39, 39, 39, 39, 20, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/145 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1) `ZINC001118777913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118777913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118777913 none CCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 21, 21, 21, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 40, 40, 40, 40, 40, 21, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118777913 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 Building ZINC001118777913 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118777913 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 144) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1) `ZINC001118777913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118777913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118777913 none CCn1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 20, 20, 20, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 20, 20, 39, 39, 39, 39, 39, 20, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 145) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1) `ZINC001118777913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118777913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001118777913 none CCn1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 21, 21, 21, 12, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 40, 40, 40, 40, 40, 21, 12, 12, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118777913 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118777913 Building ZINC001118797136 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118797136 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/146 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc(O)o1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118797136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118797136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001118797136 none CN(Cc1nnc(O)o1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 12, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 15, 33, 33, 33, 33, 33, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 99, 5, 5, 5, 5, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/147 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc(O)o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118797136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118797136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001118797136 none CN(Cc1nnc(O)o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 12, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 17, 31, 31, 31, 31, 31, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 17, 17, 93, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118797136 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 Building ZINC001118797136 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118797136 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 146) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc(O)o1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118797136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118797136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001118797136 none CN(Cc1nnc(O)o1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 12, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 15, 33, 33, 33, 33, 33, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 99, 5, 5, 5, 5, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 147) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1nnc(O)o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001118797136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118797136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001118797136 none CN(Cc1nnc(O)o1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 8, 1, 12, 12, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 17, 31, 31, 31, 31, 31, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 17, 17, 93, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118797136 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118797136 Building ZINC001118887910 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118887910 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/148 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC001118887910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118887910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118887910 none CSCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 17, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 7, 7, 38, 38, 38, 17, 17, 17, 17, 3, 6, 6, 6, 6, 6, 7, 7] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/149 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC001118887910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118887910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118887910 none CSCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 15, 13, 5, 2, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 37, 37, 37, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118887910 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 Building ZINC001118887910 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118887910 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 148) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC001118887910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118887910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118887910 none CSCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 17, 16, 6, 3, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 7, 7, 38, 38, 38, 17, 17, 17, 17, 3, 6, 6, 6, 6, 6, 7, 7] 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 149) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O) `ZINC001118887910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118887910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001118887910 none CSCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 15, 13, 5, 2, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 5, 5, 5, 37, 37, 37, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118887910 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118887910 Building ZINC001118911775 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118911775 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/150 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1) `ZINC001118911775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118911775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118911775 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 19, 19, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 19, 19, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/151 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1) `ZINC001118911775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118911775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118911775 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 21, 21, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 21, 21, 12] 49 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118911775 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 Building ZINC001118911775 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118911775 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 150) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1) `ZINC001118911775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118911775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118911775 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 19, 19, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 19, 19, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 151) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1) `ZINC001118911775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118911775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001118911775 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H]2C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 15, 15, 21, 21, 12, 12, 12, 12, 12, 12, 15, 15, 15, 15, 15, 15, 21, 21, 12] 49 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118911775 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118911775 Building ZINC001118959546 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118959546 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/152 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC001118959546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118959546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118959546 none O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 4, 19, 19, 19, 37, 19, 37, 19, 1, 1, 1, 5, 5, 5, 5, 5, 2, 19, 19, 19, 37, 37, 111, 37, 37, 111, 19, 19, 5, 5, 5] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 460 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/153 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC001118959546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118959546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118959546 none O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 4, 19, 19, 19, 37, 19, 37, 19, 1, 1, 1, 5, 5, 5, 5, 5, 2, 19, 19, 19, 37, 37, 111, 37, 37, 111, 19, 19, 5, 5, 5] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 460 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118959546 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 Building ZINC001118959546 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118959546 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 152) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccc[nH]1) `ZINC001118959546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118959546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118959546 none O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 4, 19, 19, 19, 37, 19, 37, 19, 1, 1, 1, 5, 5, 5, 5, 5, 2, 19, 19, 19, 37, 37, 111, 37, 37, 111, 19, 19, 5, 5, 5] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 460 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 153) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccc[nH]1) `ZINC001118959546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118959546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001118959546 none O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccc[nH]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 8, 6, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 4, 19, 19, 19, 37, 19, 37, 19, 1, 1, 1, 5, 5, 5, 5, 5, 2, 19, 19, 19, 37, 37, 111, 37, 37, 111, 19, 19, 5, 5, 5] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 460 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118959546 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118959546 Building ZINC001118968741 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118968741 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/154 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001118968741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118968741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118968741 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 31, 12, 12, 12, 30, 12, 6, 6, 6, 6, 6, 6, 12, 12, 31, 31, 93, 30, 30, 90, 12, 12] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 369 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/155 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001118968741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118968741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118968741 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 27, 12, 12, 12, 33, 12, 6, 6, 6, 6, 6, 6, 12, 12, 27, 27, 81, 33, 33, 99, 12, 12] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 363 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118968741 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 Building ZINC001118968741 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118968741 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 154) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001118968741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118968741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118968741 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 31, 12, 12, 12, 30, 12, 6, 6, 6, 6, 6, 6, 12, 12, 31, 31, 93, 30, 30, 90, 12, 12] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 369 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 155) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001118968741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118968741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001118968741 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 27, 12, 12, 12, 33, 12, 6, 6, 6, 6, 6, 6, 12, 12, 27, 27, 81, 33, 33, 99, 12, 12] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 363 number of broken/clashed sets: 75 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118968741 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118968741 Building ZINC001118981038 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118981038 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/156 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1) `ZINC001118981038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118981038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001118981038 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 11, 12, 12, 12, 12, 27, 27, 27, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 27, 50, 50, 50, 50, 150, 12, 12, 12, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/157 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1) `ZINC001118981038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118981038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001118981038 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 12, 12, 12, 12, 12, 26, 26, 26, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 26, 50, 50, 50, 50, 150, 12, 12, 12, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118981038 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 Building ZINC001118981038 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001118981038 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 156) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1) `ZINC001118981038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001118981038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001118981038 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 11, 12, 12, 12, 12, 27, 27, 27, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 27, 50, 50, 50, 50, 150, 12, 12, 12, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 157) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1) `ZINC001118981038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001118981038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001118981038 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCCO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 12, 12, 12, 12, 12, 26, 26, 26, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 26, 50, 50, 50, 50, 150, 12, 12, 12, 12] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001118981038 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001118981038 Building ZINC001119056092 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119056092 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/158 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O) `ZINC001119056092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119056092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001119056092 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 22, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 45, 45, 45, 45, 45, 45, 135] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 248 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/159 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O) `ZINC001119056092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119056092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001119056092 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 22, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 44, 44, 132] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 243 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119056092 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 Building ZINC001119056092 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119056092 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 158) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O) `ZINC001119056092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119056092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001119056092 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 22, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 45, 45, 45, 45, 45, 45, 135] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 248 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 159) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O) `ZINC001119056092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119056092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001119056092 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COCC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 22, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 44, 44, 132] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 243 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119056092 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119056092 Building ZINC001119057806 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119057806 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/160 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1) `ZINC001119057806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119057806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001119057806 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 22, 22, 22, 22, 22, 8, 4, 13, 13, 13, 13, 13, 13, 39, 8] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/161 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1) `ZINC001119057806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119057806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001119057806 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 24, 24, 24, 24, 24, 8, 4, 11, 11, 11, 11, 11, 11, 33, 8] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119057806 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 Building ZINC001119057806 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119057806 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 160) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1) `ZINC001119057806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119057806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001119057806 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 22, 22, 22, 22, 22, 8, 4, 13, 13, 13, 13, 13, 13, 39, 8] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 161) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1) `ZINC001119057806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119057806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001119057806 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCOC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 8, 8, 8, 1, 1, 1, 1, 4, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 24, 24, 24, 24, 24, 8, 4, 11, 11, 11, 11, 11, 11, 33, 8] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119057806 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119057806 Building ZINC001119279133 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119279133 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/162 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001119279133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119279133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119279133 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 22, 22, 22, 22, 22, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 22, 9, 9, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/163 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001119279133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119279133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119279133 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 21, 21, 21, 21, 21, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 21, 9, 9, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119279133 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 Building ZINC001119279133 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119279133 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 162) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001119279133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119279133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119279133 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 22, 22, 22, 22, 22, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 22, 9, 9, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 163) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001119279133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119279133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119279133 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 21, 21, 21, 21, 21, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 34, 34, 34, 34, 34, 21, 9, 9, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119279133 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119279133 Building ZINC001119289845 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119289845 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/164 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1) `ZINC001119289845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119289845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119289845 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/165 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1) `ZINC001119289845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119289845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119289845 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119289845 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 Building ZINC001119289845 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119289845 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 164) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1) `ZINC001119289845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119289845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119289845 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 165) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1) `ZINC001119289845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119289845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001119289845 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3ncncc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 1, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 6, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119289845 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119289845 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/168' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/169' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/170' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/171' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/172' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/173' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454384 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454384 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 166) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 167) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 168) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 169) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 24, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 13, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 88 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 170) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 171) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 172) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454384.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 173) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454384.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454384 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 32, 32, 32, 32, 32, 32, 32, 32, 15, 15, 15, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 93 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454384 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454384 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/176' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/177' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/178' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/179' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/180' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/181' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454385 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454385 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 174) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 175) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 176) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 177) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 178) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 179) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 180) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454385.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 33, 33, 33, 33, 33, 33, 33, 33, 16, 16, 16, 5, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 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]) total number of confs: 109 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 181) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454385.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454385 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454385 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/184' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/185' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/186' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/187' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/188' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/189' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454386 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454386 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 182) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 183) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 184) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 185) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 24, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 15, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 186) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 187) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 188) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C) `ZINC001119454386.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 13, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 23, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 13, 3, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29] 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]) total number of confs: 86 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 189) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C) `ZINC001119454386.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454386 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 14, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 24, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 3, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 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]) total number of confs: 91 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454386 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454386 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/192' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/193' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/194' -> `4.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/195' -> `5.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/196' -> `6.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/197' -> `7.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119454387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 8 protomers extracted for ZINC001119454387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 190) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 191) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 192) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 23, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 106 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 193) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 22, 32, 32, 32, 32, 32, 32, 32, 32, 16, 16, 16, 5, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 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]) total number of confs: 107 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `4' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 4 (index: 194) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 4 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `4.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `4.mol2' -> `4.mol2.original' `output.mol2' -> `4.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `5' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 5 (index: 195) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 5 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `5.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `5.mol2' -> `5.mol2.original' `output.mol2' -> `5.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `6' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 6 (index: 196) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 6 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C) `ZINC001119454387.mol2' -> `6.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `6.mol2' -> `6.mol2.original' `output.mol2' -> `6.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `7' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 7 (index: 197) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 7 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C) `ZINC001119454387.mol2' -> `7.mol2' `temp.mol2' -> `ZINC001119454387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `7.mol2' -> `7.mol2.original' `output.mol2' -> `7.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001119454387 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)[C@H]1C[N@](C)CC[N@]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 5, 10, 5, 5, 5, 10, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 16, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 25, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 5, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119454387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/3.* 5: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/5.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/1.* 6: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/6.* 4: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/4.* 7: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/7.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119454387 Building ZINC001119548757 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119548757 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/198 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1) `ZINC001119548757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119548757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119548757 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 11, 11, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 19, 19, 19, 19, 19, 7, 4, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/199 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1) `ZINC001119548757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119548757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119548757 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 11, 11, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 4, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119548757 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 Building ZINC001119548757 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119548757 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 198) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1) `ZINC001119548757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119548757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119548757 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 11, 11, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 7, 7, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 19, 19, 19, 19, 19, 7, 4, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 199) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1) `ZINC001119548757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119548757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119548757 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CS(=O)(=O)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 14, 11, 11, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 20, 20, 20, 20, 20, 6, 4, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119548757 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119548757 Building ZINC001119592024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119592024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/200 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1) `ZINC001119592024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119592024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592024 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 32, 32, 32, 35, 35, 32, 35, 35, 6, 6, 6, 6, 6, 6, 4, 17, 17, 96, 35, 35, 35, 35, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 252 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/201 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1) `ZINC001119592024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119592024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592024 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 4, 18, 18, 96, 34, 34, 34, 34, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119592024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 Building ZINC001119592024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119592024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 200) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1) `ZINC001119592024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119592024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592024 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 17, 32, 32, 32, 35, 35, 32, 35, 35, 6, 6, 6, 6, 6, 6, 4, 17, 17, 96, 35, 35, 35, 35, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 252 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 201) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1) `ZINC001119592024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119592024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592024 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 8, 4, 18, 18, 96, 34, 34, 34, 34, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 240 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119592024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592024 Building ZINC001119592025 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119592025 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/202 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1) `ZINC001119592025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119592025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592025 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 34, 34, 33, 34, 34, 8, 8, 8, 8, 8, 8, 4, 18, 18, 96, 34, 34, 34, 34, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/203 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1) `ZINC001119592025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119592025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592025 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 33, 33, 33, 38, 38, 33, 38, 38, 6, 6, 6, 6, 6, 6, 4, 18, 18, 99, 38, 38, 38, 38, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119592025 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 Building ZINC001119592025 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119592025 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 202) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1) `ZINC001119592025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119592025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592025 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 18, 32, 32, 32, 34, 34, 33, 34, 34, 8, 8, 8, 8, 8, 8, 4, 18, 18, 96, 34, 34, 34, 34, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 243 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 203) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1) `ZINC001119592025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119592025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001119592025 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 18, 33, 33, 33, 38, 38, 33, 38, 38, 6, 6, 6, 6, 6, 6, 4, 18, 18, 99, 38, 38, 38, 38, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119592025 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119592025 Building ZINC001119607219 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119607219 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/204 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1) `ZINC001119607219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119607219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119607219 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/205 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1) `ZINC001119607219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119607219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119607219 none CCn1cc([C@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119607219 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 Building ZINC001119607219 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119607219 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 204) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1) `ZINC001119607219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119607219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119607219 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 205) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1) `ZINC001119607219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119607219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001119607219 none CCn1cc([C@]([O-])([SiH3])C(=O)N2Cc3nn(C)c(N)c3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 20, 20, 20, 20, 20, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119607219 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119607219 Building ZINC001119624198 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119624198 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/206 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1) `ZINC001119624198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119624198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624198 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 29, 36, 36, 6, 6, 6, 6, 6, 6, 2, 13, 13, 24, 24, 26, 29, 36, 36, 36, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/207 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1) `ZINC001119624198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119624198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624198 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 17, 24, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 22, 22, 22, 24, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119624198 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 Building ZINC001119624198 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119624198 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 206) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1) `ZINC001119624198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119624198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624198 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 21, 29, 36, 36, 6, 6, 6, 6, 6, 6, 2, 13, 13, 24, 24, 26, 29, 36, 36, 36, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 207) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1) `ZINC001119624198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119624198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624198 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 17, 24, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 22, 22, 22, 24, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119624198 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624198 Building ZINC001119624199 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119624199 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/208 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1) `ZINC001119624199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119624199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624199 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 17, 24, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 22, 22, 24, 22, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/209 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1) `ZINC001119624199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119624199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624199 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 19, 27, 34, 34, 6, 6, 6, 6, 6, 6, 2, 12, 12, 22, 22, 27, 24, 34, 34, 34, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119624199 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 Building ZINC001119624199 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001119624199 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 208) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1) `ZINC001119624199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001119624199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624199 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 17, 24, 32, 32, 6, 6, 6, 6, 6, 6, 2, 14, 14, 22, 22, 24, 22, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 209) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1) `ZINC001119624199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001119624199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001119624199 none Cn1cc([C@]([O-])([SiH3])C(=O)NCCC[S@@](C)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'S.o', 'C.3', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 14, 5, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 19, 27, 34, 34, 6, 6, 6, 6, 6, 6, 2, 12, 12, 22, 22, 27, 24, 34, 34, 34, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001119624199 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001119624199 Building ZINC001120819737 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001120819737 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/210 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/210' -> `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)NCc1cnnn1C) `ZINC001120819737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001120819737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001120819737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 21, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 21, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/211 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnnn1C) `ZINC001120819737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001120819737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001120819737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001120819737 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 Building ZINC001120819737 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001120819737 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 210) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnnn1C) `ZINC001120819737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001120819737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001120819737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 21, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 21, 21, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 211) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnnn1C) `ZINC001120819737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001120819737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001120819737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 20, 46, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 20, 20, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001120819737 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120819737 Building ZINC001120851862 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001120851862 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/212 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1) `ZINC001120851862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001120851862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851862 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 9, 25, 25, 25, 25, 25, 25, 25, 25, 24, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/213 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1) `ZINC001120851862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001120851862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851862 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 9, 26, 27, 27, 27, 27, 27, 27, 27, 24, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001120851862 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 Building ZINC001120851862 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001120851862 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 212) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1) `ZINC001120851862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001120851862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851862 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 9, 25, 25, 25, 25, 25, 25, 25, 25, 24, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 213) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1) `ZINC001120851862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001120851862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851862 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 9, 26, 27, 27, 27, 27, 27, 27, 27, 24, 10, 10, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001120851862 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851862 Building ZINC001120851863 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001120851863 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/214 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1) `ZINC001120851863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001120851863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851863 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26, 26, 22, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/215 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1) `ZINC001120851863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001120851863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851863 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26, 26, 25, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001120851863 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 Building ZINC001120851863 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001120851863 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 214) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1) `ZINC001120851863.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001120851863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851863 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26, 26, 22, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 215) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1) `ZINC001120851863.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001120851863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001120851863 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]3(CCOC3=O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 12, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 4, 8, 26, 26, 26, 26, 26, 26, 26, 26, 25, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001120851863 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001120851863 Building ZINC001121228292 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001121228292 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/216 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1) `ZINC001121228292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001121228292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228292 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 34, 32, 39, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 38, 39, 117, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/217 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1) `ZINC001121228292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001121228292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228292 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 38, 36, 42, 38, 48, 49, 49, 48, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 42, 42, 126, 48, 49, 48, 49] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001121228292 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 Building ZINC001121228292 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001121228292 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 216) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1) `ZINC001121228292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001121228292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228292 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 34, 32, 39, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 38, 39, 117, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 217) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1) `ZINC001121228292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001121228292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228292 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 38, 36, 42, 38, 48, 49, 49, 48, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 42, 42, 126, 48, 49, 48, 49] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001121228292 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228292 Building ZINC001121228293 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001121228293 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/218 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1) `ZINC001121228293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001121228293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228293 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 38, 36, 42, 38, 48, 49, 49, 48, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 42, 42, 126, 48, 49, 48, 49] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/219 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1) `ZINC001121228293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001121228293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228293 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 34, 32, 39, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 39, 38, 117, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 353 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001121228293 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 Building ZINC001121228293 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001121228293 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 218) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1) `ZINC001121228293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001121228293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228293 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 38, 36, 42, 38, 48, 49, 49, 48, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 42, 42, 126, 48, 49, 48, 49] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 219) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1) `ZINC001121228293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001121228293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001121228293 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Nc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 4, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 34, 32, 39, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 39, 38, 117, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 353 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001121228293 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121228293 Building ZINC001121245755 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001121245755 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/220 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/220' -> `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)Nc1cnn(C)c(=O)c1) `ZINC001121245755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001121245755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001121245755 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 33, 33, 33, 33, 33] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/221 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1) `ZINC001121245755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001121245755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001121245755 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 36, 36, 36, 36, 36] 43 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001121245755 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 Building ZINC001121245755 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001121245755 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 220) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1) `ZINC001121245755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001121245755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001121245755 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 33, 33, 33, 33, 33] 39 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 221) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1) `ZINC001121245755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001121245755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001121245755 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c(=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 9, 36, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 36, 36, 36, 36, 36] 43 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001121245755 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001121245755 Building ZINC001122030252 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122030252 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/222 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1) `ZINC001122030252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122030252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122030252 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 6, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/223 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1) `ZINC001122030252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122030252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122030252 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 6, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122030252 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 Building ZINC001122030252 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122030252 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 222) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1) `ZINC001122030252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122030252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122030252 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 6, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 223) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1) `ZINC001122030252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122030252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122030252 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCNC[C@@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 10, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 6, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122030252 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122030252 Building ZINC001122073275 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122073275 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/224 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122073275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073275 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 32, 13, 20, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 20, 22, 32, 32, 32, 32, 32, 32, 32, 13, 13, 3, 7, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/225 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122073275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073275 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 30, 13, 20, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 20, 23, 30, 30, 30, 30, 30, 30, 30, 13, 13, 3, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122073275 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 Building ZINC001122073275 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122073275 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 224) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122073275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073275 none CC(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 32, 13, 20, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 20, 22, 32, 32, 32, 32, 32, 32, 32, 13, 13, 3, 7, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 225) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122073275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073275 none CC(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 30, 13, 20, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 20, 23, 30, 30, 30, 30, 30, 30, 30, 13, 13, 3, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122073275 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073275 Building ZINC001122073276 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122073276 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/226 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122073276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073276 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 15, 22, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 22, 24, 29, 29, 29, 29, 29, 29, 29, 15, 15, 3, 8, 8, 8, 8, 8, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/227 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122073276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073276 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 31, 16, 22, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 22, 23, 31, 31, 31, 31, 31, 31, 31, 16, 16, 4, 7, 7, 7, 7, 7, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122073276 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 Building ZINC001122073276 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122073276 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 226) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122073276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073276 none CC(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 29, 15, 22, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 22, 24, 29, 29, 29, 29, 29, 29, 29, 15, 15, 3, 8, 8, 8, 8, 8, 24, 24] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 227) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON) `ZINC001122073276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122073276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001122073276 none CC(C)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)ON NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 31, 16, 22, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 22, 23, 31, 31, 31, 31, 31, 31, 31, 16, 16, 4, 7, 7, 7, 7, 7, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122073276 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122073276 Building ZINC001122100716 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122100716 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/228 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122100716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100716 none CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 14, 9, 14, 14, 5, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 23, 23, 23, 23, 20, 20, 42, 9, 9, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/229 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122100716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100716 none CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 10, 9, 10, 10, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 19, 19, 19, 19, 18, 18, 30, 9, 9, 5, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122100716 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 Building ZINC001122100716 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122100716 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 228) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122100716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100716 none CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 20, 14, 9, 14, 14, 5, 3, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 23, 23, 23, 23, 20, 20, 42, 9, 9, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 161 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 229) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122100716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100716 none CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 10, 9, 10, 10, 5, 2, 5, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 4, 19, 19, 19, 19, 18, 18, 30, 9, 9, 5, 5, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122100716 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100716 Building ZINC001122100717 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122100717 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/230 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122100717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100717 none CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 20, 20, 20, 20, 16, 16, 30, 7, 7, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/231 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122100717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100717 none CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 11, 7, 11, 11, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 23, 23, 23, 23, 18, 18, 33, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122100717 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 Building ZINC001122100717 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122100717 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 230) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122100717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100717 none CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 16, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 20, 20, 20, 20, 16, 16, 30, 7, 7, 3, 3, 3, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 156 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 231) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC001122100717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122100717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001122100717 none CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 11, 7, 11, 11, 4, 2, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 23, 23, 23, 23, 18, 18, 33, 7, 7, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 158 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122100717 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122100717 Building ZINC001122182640 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122182640 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/232 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2) `ZINC001122182640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122182640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001122182640 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 3, 14, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 21 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/233 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2) `ZINC001122182640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122182640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001122182640 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 3, 13, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122182640 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 Building ZINC001122182640 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122182640 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 232) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2) `ZINC001122182640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122182640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001122182640 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 3, 14, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 21 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 233) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2) `ZINC001122182640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122182640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001122182640 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1NC(=O)CC12CCNCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 3, 13, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [1, 4, 5] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 40 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122182640 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122182640 Building ZINC001122233825 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122233825 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/234 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001122233825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122233825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001122233825 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 27, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/235 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001122233825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122233825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001122233825 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122233825 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 Building ZINC001122233825 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001122233825 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 234) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001122233825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122233825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001122233825 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 8, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 27, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 235) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1) `ZINC001122233825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122233825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001122233825 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC3(CC2)CNCCO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 7, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6, 6, 6, 28, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122233825 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122233825 Building ZINC001122522036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001122522036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/236 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/237 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/238 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/238' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/239 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/239' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122522036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 Building ZINC001122522036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001122522036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 236) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 237) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 238) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 239) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122522036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 Building ZINC001122522036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001122522036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 236) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 237) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 238) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 239) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122522036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 Building ZINC001122522036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001122522036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 236) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 237) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 238) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 9, 26, 26, 26, 26, 26, 26, 23, 10, 10, 10, 10, 10, 10, 4, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 239) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1) `ZINC001122522036.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001122522036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001122522036 none Cn1cc([C@]([O-])([SiH3])C(=O)NC2CC3(CC(N)C3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 4, 4, 10, 27, 27, 27, 27, 27, 27, 23, 10, 10, 10, 10, 10, 10, 4, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001122522036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001122522036 Building ZINC001123869182 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123869182 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/240 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1) `ZINC001123869182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123869182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869182 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 7, 20, 20, 20, 20, 20, 43, 43, 43, 43, 43, 20, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/241 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1) `ZINC001123869182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123869182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869182 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 44, 44, 44, 44, 44, 19, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123869182 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 Building ZINC001123869182 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123869182 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 240) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1) `ZINC001123869182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123869182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869182 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 4, 7, 20, 20, 20, 20, 20, 43, 43, 43, 43, 43, 20, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 241) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1) `ZINC001123869182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123869182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869182 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 8, 19, 19, 19, 19, 19, 44, 44, 44, 44, 44, 19, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123869182 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869182 Building ZINC001123869186 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123869186 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/242 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1) `ZINC001123869186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123869186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869186 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 8, 20, 20, 20, 20, 20, 44, 44, 44, 44, 44, 20, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/243 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1) `ZINC001123869186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123869186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869186 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 7, 20, 20, 20, 20, 20, 39, 39, 39, 39, 39, 20, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123869186 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 Building ZINC001123869186 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123869186 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 242) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1) `ZINC001123869186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123869186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869186 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 8, 20, 20, 20, 20, 20, 44, 44, 44, 44, 44, 20, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 243) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1) `ZINC001123869186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123869186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001123869186 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2nn[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 1, 8, 8, 8, 6, 8, 5, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 7, 20, 20, 20, 20, 20, 39, 39, 39, 39, 39, 20, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 71 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123869186 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123869186 Building ZINC001123879006 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123879006 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/244 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C1(O)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001123879006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123879006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001123879006 none Cn1nncc1C1(O)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 69, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 150 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 36, 35]) total number of confs: 146 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/245 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001123879006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123879006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001123879006 none Cn1nncc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 2, 2, 2, 23, 50, 50, 50, 50, 69, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123879006 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 Building ZINC001123879006 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123879006 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 244) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C1(O)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001123879006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123879006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001123879006 none Cn1nncc1C1(O)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 69, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 150 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 36, 35]) total number of confs: 146 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 245) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001123879006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123879006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001123879006 none Cn1nncc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 2, 2, 2, 23, 50, 50, 50, 50, 69, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123879006 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123879006 Building ZINC001123964011 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123964011 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/246 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1) `ZINC001123964011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123964011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001123964011 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 1, 2, 4, 13, 13, 13, 23, 23, 23, 13, 5, 5, 20, 20, 20, 20, 20, 5, 13, 13, 13, 23, 23, 23, 69, 13, 13, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/247 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1) `ZINC001123964011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123964011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001123964011 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 4, 4, 1, 1, 1, 1, 2, 4, 12, 12, 12, 19, 19, 19, 12, 4, 4, 15, 15, 15, 15, 15, 4, 12, 12, 12, 19, 19, 19, 57, 12, 12, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 158 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123964011 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 Building ZINC001123964011 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001123964011 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 246) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1) `ZINC001123964011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001123964011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001123964011 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 5, 5, 5, 1, 1, 1, 1, 2, 4, 13, 13, 13, 23, 23, 23, 13, 5, 5, 20, 20, 20, 20, 20, 5, 13, 13, 13, 23, 23, 23, 69, 13, 13, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 196 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 247) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1) `ZINC001123964011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001123964011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001123964011 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC([C@H](C)O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 4, 4, 1, 1, 1, 1, 2, 4, 12, 12, 12, 19, 19, 19, 12, 4, 4, 15, 15, 15, 15, 15, 4, 12, 12, 12, 19, 19, 19, 57, 12, 12, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 158 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001123964011 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001123964011 Building ZINC001124003401 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124003401 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/248 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1) `ZINC001124003401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124003401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001124003401 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 21, 38, 38, 38, 38, 38, 38, 38, 21, 21, 21, 7, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/249 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1) `ZINC001124003401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124003401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001124003401 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 22, 7, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124003401 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 Building ZINC001124003401 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124003401 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 248) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1) `ZINC001124003401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124003401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001124003401 none CN(C(=O)[C@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 21, 38, 38, 38, 38, 38, 38, 38, 21, 21, 21, 7, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 249) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1) `ZINC001124003401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124003401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001124003401 none CN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)N1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 7, 7, 7, 7, 7, 22, 38, 38, 38, 38, 38, 38, 38, 22, 22, 22, 7, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124003401 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124003401 Building ZINC001124966697 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124966697 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/250 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124966697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966697 none CCN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 33, 35, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 30, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/251 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124966697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966697 none CCN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 30, 34, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 34, 27, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124966697 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 Building ZINC001124966697 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124966697 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 250) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124966697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966697 none CCN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 33, 35, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 30, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 251) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124966697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966697 none CCN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 30, 34, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 34, 27, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124966697 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966697 Building ZINC001124966698 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124966698 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/252 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124966698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966698 none CCN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 28, 30, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 30, 30, 30, 30, 25, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/253 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124966698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966698 none CCN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 33, 35, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 28, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124966698 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 Building ZINC001124966698 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124966698 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 252) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124966698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966698 none CCN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 28, 30, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 30, 30, 30, 30, 25, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 253) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124966698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124966698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124966698 none CCN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 35, 33, 35, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 28, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124966698 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966698 Building ZINC001124966816 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124966816 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/254 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001124966816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124966816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124966816 none Cc1nc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 28, 15, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 28, 28, 15, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/255 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001124966816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124966816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124966816 none Cc1nc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 15, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 15, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124966816 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 Building ZINC001124966816 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124966816 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 254) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001124966816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124966816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124966816 none Cc1nc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 28, 15, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 28, 28, 15, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 255) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1) `ZINC001124966816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124966816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124966816 none Cc1nc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 15, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 30, 30, 15, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124966816 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124966816 Building ZINC001124967104 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967104 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/256 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1) `ZINC001124967104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124967104 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 12, 20, 21, 28, 28, 28, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 12, 20, 20, 21, 21, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/257 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1) `ZINC001124967104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124967104 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 18, 19, 33, 33, 33, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 13, 18, 18, 19, 19, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967104 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 Building ZINC001124967104 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967104 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 256) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1) `ZINC001124967104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124967104 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 12, 20, 21, 28, 28, 28, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 12, 20, 20, 21, 21, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 257) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1) `ZINC001124967104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124967104 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCNC(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 8, 13, 18, 19, 33, 33, 33, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 8, 8, 13, 18, 18, 19, 19, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967104 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967104 Building ZINC001124967476 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967476 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/258 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1cnon1) `ZINC001124967476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001124967476 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1cnon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 26, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 26, 42, 42, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/259 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1cnon1) `ZINC001124967476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001124967476 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1cnon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 25, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 17, 25, 42, 42, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967476 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 Building ZINC001124967476 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967476 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 258) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1cnon1) `ZINC001124967476.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001124967476 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1cnon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 26, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 26, 42, 42, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 259) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1cnon1) `ZINC001124967476.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001124967476 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1cnon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 17, 25, 42, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 17, 17, 25, 42, 42, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967476 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967476 Building ZINC001124967614 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967614 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/260 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O) `ZINC001124967614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124967614 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 24, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/261 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O) `ZINC001124967614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124967614 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 24, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967614 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 Building ZINC001124967614 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967614 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 260) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O) `ZINC001124967614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124967614 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 24, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 261) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O) `ZINC001124967614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124967614 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 38, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 24, 38, 38, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967614 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967614 Building ZINC001124967756 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967756 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/262 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967756 none C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 39, 48, 24, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 39, 24, 24, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 205 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/263 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967756 none C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 21, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 36, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967756 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 Building ZINC001124967756 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967756 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 262) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967756 none C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 39, 48, 24, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 39, 24, 24, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 205 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 263) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967756 none C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 21, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 36, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967756 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967756 Building ZINC001124967758 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967758 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/264 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967758 none C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 21, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 36, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/265 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967758 none C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 38, 48, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 38, 24, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967758 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 Building ZINC001124967758 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967758 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 264) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967758 none C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 46, 21, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 46, 46, 46, 36, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 265) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001124967758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124967758 none C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 38, 48, 24, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 38, 24, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967758 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967758 Building ZINC001124967922 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967922 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/266 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124967922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124967922 none Cn1ncc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 23, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 23, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/267 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124967922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124967922 none Cn1ncc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 20, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 20, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967922 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 Building ZINC001124967922 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124967922 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 266) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124967922.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124967922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124967922 none Cn1ncc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 23, 14, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 23, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 267) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124967922.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124967922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124967922 none Cn1ncc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 20, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 40, 40, 20, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124967922 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124967922 Building ZINC001124968264 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124968264 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/268 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124968264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124968264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124968264 none CCCn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 39, 39, 39, 39, 39, 32, 23, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 32, 32, 23, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/269 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124968264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124968264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124968264 none CCCn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 36, 36, 36, 36, 36, 28, 20, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 28, 28, 20, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124968264 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 Building ZINC001124968264 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124968264 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 268) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124968264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124968264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124968264 none CCCn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 39, 39, 39, 39, 39, 32, 23, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 32, 32, 23, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 269) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124968264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124968264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124968264 none CCCn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 36, 36, 36, 36, 36, 28, 20, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 49, 49, 28, 28, 20, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124968264 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124968264 Building ZINC001124971514 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124971514 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/270 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCn1cncn1) `ZINC001124971514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124971514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124971514 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 31, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 20, 31, 31, 32, 32, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/271 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCn1cncn1) `ZINC001124971514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124971514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124971514 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 31, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 20, 31, 31, 32, 32, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124971514 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 Building ZINC001124971514 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124971514 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 270) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCn1cncn1) `ZINC001124971514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124971514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124971514 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 31, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 20, 31, 31, 32, 32, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 271) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCn1cncn1) `ZINC001124971514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124971514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124971514 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 20, 31, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 14, 14, 20, 31, 31, 32, 32, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124971514 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971514 Building ZINC001124971553 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124971553 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/272 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1) `ZINC001124971553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124971553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124971553 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 28, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 28, 46, 46, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/273 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1) `ZINC001124971553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124971553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124971553 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 18, 26, 38, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 18, 18, 26, 38, 38, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124971553 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 Building ZINC001124971553 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124971553 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 272) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1) `ZINC001124971553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124971553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124971553 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 28, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 28, 46, 46, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 273) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1) `ZINC001124971553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124971553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124971553 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)Nc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 18, 26, 38, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 18, 18, 26, 38, 38, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124971553 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971553 Building ZINC001124971652 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124971652 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/274 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1) `ZINC001124971652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124971652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124971652 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 28, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/275 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1) `ZINC001124971652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124971652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124971652 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 15, 28, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 15, 15, 28, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124971652 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 Building ZINC001124971652 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124971652 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 274) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1) `ZINC001124971652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124971652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124971652 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 28, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 28, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 275) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1) `ZINC001124971652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124971652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124971652 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 15, 28, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 15, 15, 28, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124971652 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124971652 Building ZINC001124972047 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972047 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/276 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972047 none C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 37, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 41, 50, 50, 37, 37, 37, 27, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/277 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972047 none C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 34, 34, 34, 50, 50, 31, 31, 31, 20, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972047 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 Building ZINC001124972047 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972047 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 276) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972047 none C[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 37, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 41, 50, 50, 37, 37, 37, 27, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 277) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972047 none C[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 31, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 34, 34, 34, 50, 50, 31, 31, 31, 20, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 206 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972047 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972047 Building ZINC001124972048 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972048 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/278 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972048 none C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 38, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 40, 40, 40, 50, 50, 38, 38, 38, 30, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/279 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972048 none C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 37, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 41, 50, 50, 37, 37, 37, 27, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972048 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 Building ZINC001124972048 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972048 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 278) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972048 none C[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 38, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 40, 40, 40, 50, 50, 38, 38, 38, 30, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 279) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1) `ZINC001124972048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001124972048 none C[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 37, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 41, 41, 41, 50, 50, 37, 37, 37, 27, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 7, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972048 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972048 Building ZINC001124972648 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972648 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/280 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972648 none CN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 26, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/281 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972648 none CN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 50, 27, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 27, 27, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972648 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 Building ZINC001124972648 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972648 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 280) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972648 none CN1CC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 26, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 26, 26, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 281) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972648 none CN1CC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 50, 27, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 27, 27, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972648 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972648 Building ZINC001124972649 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972649 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/282 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972649 none CN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 50, 25, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 25, 25, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/283 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972649 none CN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 25, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972649 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 Building ZINC001124972649 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972649 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 282) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972649 none CN1CC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 50, 25, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 25, 25, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 283) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124972649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124972649 none CN1CC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 50, 25, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972649 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972649 Building ZINC001124972814 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972814 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/284 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O) `ZINC001124972814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124972814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 36, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 24, 36, 36, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/285 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O) `ZINC001124972814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124972814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 12, 23, 35, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 23, 35, 35, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972814 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 Building ZINC001124972814 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124972814 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 284) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O) `ZINC001124972814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124972814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124972814 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 14, 24, 36, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 14, 14, 24, 36, 36, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 285) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O) `ZINC001124972814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124972814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124972814 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 12, 23, 35, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 12, 12, 23, 35, 35, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124972814 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124972814 Building ZINC001124976412 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976412 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/286 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O) `ZINC001124976412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976412 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 21, 21, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/287 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O) `ZINC001124976412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976412 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 21, 21, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976412 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 Building ZINC001124976412 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976412 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 286) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O) `ZINC001124976412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976412 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 21, 34, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 21, 21, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 287) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O) `ZINC001124976412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976412 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 21, 21, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976412 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976412 Building ZINC001124976413 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976413 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/288 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O) `ZINC001124976413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976413 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 21, 21, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/289 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O) `ZINC001124976413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976413 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976413 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 Building ZINC001124976413 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976413 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 288) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O) `ZINC001124976413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976413 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 21, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 21, 21, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 289) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O) `ZINC001124976413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001124976413 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 32, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 20, 32, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976413 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976413 Building ZINC001124976444 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976444 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/290 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001124976444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976444 none Cn1cc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 24, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 24, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/291 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001124976444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976444 none Cn1cc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 27, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 27, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976444 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 Building ZINC001124976444 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976444 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 290) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001124976444.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976444 none Cn1cc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 24, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 24, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 291) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001124976444.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976444 none Cn1cc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 27, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 45, 27, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976444 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976444 Building ZINC001124976455 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976455 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/292 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1) `ZINC001124976455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976455 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 13, 24, 28, 28, 28, 36, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 13, 24, 24, 28, 36, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/293 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1) `ZINC001124976455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976455 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 21, 27, 27, 27, 40, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 12, 21, 21, 27, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976455 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 Building ZINC001124976455 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976455 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 292) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1) `ZINC001124976455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976455 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 8, 13, 24, 28, 28, 28, 36, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 13, 24, 24, 28, 36, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 293) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1) `ZINC001124976455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976455 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 21, 27, 27, 27, 40, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 12, 21, 21, 27, 40, 40, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976455 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976455 Building ZINC001124976504 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976504 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/294 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124976504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976504 none Cn1nncc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 30, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 40, 30, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/295 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124976504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976504 none Cn1nncc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 26, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 41, 41, 26, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976504 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 Building ZINC001124976504 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976504 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 294) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124976504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976504 none Cn1nncc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 30, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 40, 30, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 295) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nncc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124976504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124976504 none Cn1nncc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 26, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 41, 41, 26, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976504 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976504 Building ZINC001124976575 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976575 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/296 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1) `ZINC001124976575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001124976575 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 18, 33, 44, 44, 44, 44, 44, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 10, 10, 18, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/297 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1) `ZINC001124976575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001124976575 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 19, 31, 43, 43, 43, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 19, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976575 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 Building ZINC001124976575 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976575 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 296) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1) `ZINC001124976575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001124976575 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 10, 18, 33, 44, 44, 44, 44, 44, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 10, 10, 18, 33, 33, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 297) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1) `ZINC001124976575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001124976575 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nnnn1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 8, 8, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 12, 19, 31, 43, 43, 43, 43, 43, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 12, 12, 19, 31, 31, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976575 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976575 Building ZINC001124976591 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976591 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/298 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1) `ZINC001124976591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001124976591 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 32, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 20, 20, 32, 49, 49, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/299 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1) `ZINC001124976591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001124976591 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 35, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 35, 49, 49, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976591 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 Building ZINC001124976591 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976591 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 298) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1) `ZINC001124976591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001124976591 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 32, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 20, 20, 32, 49, 49, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 299) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1) `ZINC001124976591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001124976591 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 35, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 35, 49, 49, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976591 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976591 Building ZINC001124976661 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976661 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/300 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O) `ZINC001124976661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976661 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/301 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O) `ZINC001124976661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976661 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 29, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 29, 29, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976661 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 Building ZINC001124976661 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976661 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 300) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O) `ZINC001124976661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976661 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 23, 46, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 23, 23, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 301) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O) `ZINC001124976661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976661 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 29, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 29, 29, 41, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976661 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976661 Building ZINC001124976662 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976662 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/302 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O) `ZINC001124976662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976662 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 26, 26, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/303 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O) `ZINC001124976662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976662 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976662 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 Building ZINC001124976662 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976662 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 302) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O) `ZINC001124976662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976662 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 45, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 26, 26, 42, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 303) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O) `ZINC001124976662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124976662 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 22, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 22, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976662 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976662 Building ZINC001124976695 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976695 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/304 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1) `ZINC001124976695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976695 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 20, 35, 39, 39, 39, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 20, 35, 35, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/305 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1) `ZINC001124976695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976695 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 21, 34, 37, 37, 37, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 21, 34, 34, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976695 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 Building ZINC001124976695 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976695 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 304) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1) `ZINC001124976695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976695 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 14, 20, 35, 39, 39, 39, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 14, 14, 20, 35, 35, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 305) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1) `ZINC001124976695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976695 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 21, 34, 37, 37, 37, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 21, 34, 34, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976695 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976695 Building ZINC001124976731 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976731 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/306 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1) `ZINC001124976731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001124976731 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 23, 39, 48, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 23, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/307 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1) `ZINC001124976731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001124976731 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 12, 21, 39, 48, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 12, 12, 21, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976731 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 Building ZINC001124976731 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976731 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 306) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1) `ZINC001124976731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001124976731 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 23, 39, 48, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 23, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 307) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1) `ZINC001124976731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001124976731 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 12, 21, 39, 48, 48, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 12, 12, 21, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 199 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976731 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976731 Building ZINC001124976742 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976742 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/308 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976742 none CN1CCC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 50, 22, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/309 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976742 none CN1CCC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 20, 20, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976742 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 Building ZINC001124976742 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976742 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 308) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976742 none CN1CCC[C@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 50, 22, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 309) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976742 none CN1CCC[C@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 43, 50, 20, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 20, 20, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976742 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976742 Building ZINC001124976743 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976743 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/310 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976743 none CN1CCC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 50, 22, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/311 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976743 none CN1CCC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976743 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 Building ZINC001124976743 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976743 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 310) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976743 none CN1CCC[C@@H](NCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 50, 22, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 311) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001124976743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976743 none CN1CCC[C@@H](NCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 50, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976743 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976743 Building ZINC001124976865 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976865 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/312 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001124976865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976865 none CN(C(=O)CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 29, 37, 15, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 50, 50, 44, 44, 44, 29, 29, 15, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/313 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001124976865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976865 none CN(C(=O)CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 34, 25, 34, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 43, 43, 43, 25, 25, 16, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976865 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 Building ZINC001124976865 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976865 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 312) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001124976865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976865 none CN(C(=O)CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 37, 29, 37, 15, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 50, 50, 44, 44, 44, 29, 29, 15, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 313) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001124976865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124976865 none CN(C(=O)CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 34, 25, 34, 16, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 50, 50, 43, 43, 43, 25, 25, 16, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44]) total number of confs: 201 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976865 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976865 Building ZINC001124976871 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976871 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/314 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O) `ZINC001124976871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976871 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 24, 24, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/315 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O) `ZINC001124976871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976871 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 21, 21, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976871 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 Building ZINC001124976871 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976871 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 314) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O) `ZINC001124976871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976871 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 24, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 24, 24, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 315) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O) `ZINC001124976871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976871 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 48, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 21, 21, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976871 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976871 Building ZINC001124976872 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976872 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/316 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O) `ZINC001124976872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976872 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 23, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/317 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O) `ZINC001124976872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976872 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 23, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 23, 23, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976872 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 Building ZINC001124976872 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976872 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 316) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O) `ZINC001124976872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976872 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 23, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 317) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O) `ZINC001124976872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976872 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 23, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 23, 23, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976872 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976872 Building ZINC001124976906 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976906 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/318 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1) `ZINC001124976906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976906 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 14, 24, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 14, 14, 24, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/319 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1) `ZINC001124976906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976906 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 28, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 28, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976906 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 Building ZINC001124976906 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124976906 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 318) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1) `ZINC001124976906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124976906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976906 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 14, 24, 43, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 14, 14, 24, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 319) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1) `ZINC001124976906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124976906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001124976906 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 15, 28, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 28, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124976906 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124976906 Building ZINC001124977024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/320 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124977024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977024 none Cn1ncnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 34, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 34, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/321 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124977024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977024 none Cn1ncnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 35, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 35, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 Building ZINC001124977024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 320) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124977024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977024 none Cn1ncnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 34, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 48, 48, 34, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 321) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124977024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977024 none Cn1ncnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 35, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 35, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977024 Building ZINC001124977029 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977029 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/322 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977029 none Cn1nnc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 23, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 37, 37, 23, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/323 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977029 none Cn1nnc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 38, 38, 20, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977029 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 Building ZINC001124977029 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977029 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 322) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977029 none Cn1nnc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 23, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 37, 37, 23, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 323) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977029 none Cn1nnc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 38, 38, 20, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977029 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977029 Building ZINC001124977040 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977040 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/324 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124977040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977040 none Cn1cnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/325 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124977040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977040 none Cn1cnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977040 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 Building ZINC001124977040 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977040 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 324) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124977040.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977040 none Cn1cnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 325) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124977040.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001124977040 none Cn1cnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 33, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 49, 49, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977040 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977040 Building ZINC001124977107 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977107 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/326 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124977107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977107 none Cn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 34, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 34, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/327 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124977107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977107 none Cn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 34, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 34, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977107 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 Building ZINC001124977107 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977107 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 326) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001124977107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977107 none Cn1nnnc1CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 34, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 34, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 327) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001124977107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001124977107 none Cn1nnnc1CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 34, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 48, 48, 34, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 11, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977107 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977107 Building ZINC001124977165 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977165 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/328 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1noc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001124977165 none CN(C)c1noc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 18, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 18, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/329 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1noc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001124977165 none CN(C)c1noc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 16, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 16, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977165 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 Building ZINC001124977165 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124977165 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 328) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1noc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124977165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001124977165 none CN(C)c1noc(CNCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 35, 18, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 35, 35, 18, 8, 8, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 329) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1noc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001124977165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124977165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001124977165 none CN(C)c1noc(CNCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 8, 12, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 34, 16, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 34, 34, 16, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124977165 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124977165 Building ZINC001124986032 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124986032 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/330 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1) `ZINC001124986032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124986032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 15, 28, 37, 37, 37, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 15, 28, 28, 111, 48, 48, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 352 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/331 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1) `ZINC001124986032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124986032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 20, 30, 40, 40, 40, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 12, 12, 20, 30, 30, 120, 47, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 362 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124986032 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 Building ZINC001124986032 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124986032 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 330) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1) `ZINC001124986032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124986032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986032 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 9, 15, 28, 37, 37, 37, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 9, 9, 15, 28, 28, 111, 48, 48, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 352 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 331) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1) `ZINC001124986032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124986032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986032 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 12, 20, 30, 40, 40, 40, 47, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 12, 12, 20, 30, 30, 120, 47, 47, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 362 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124986032 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986032 Building ZINC001124986034 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124986034 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/332 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1) `ZINC001124986034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124986034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986034 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 25, 33, 38, 38, 38, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 25, 33, 33, 114, 48, 48, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 349 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/333 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1) `ZINC001124986034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124986034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986034 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 23, 32, 39, 39, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 23, 32, 32, 117, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124986034 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 Building ZINC001124986034 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124986034 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 332) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1) `ZINC001124986034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124986034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986034 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 25, 33, 38, 38, 38, 48, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 16, 16, 25, 33, 33, 114, 48, 48, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 349 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 333) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1) `ZINC001124986034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124986034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001124986034 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNC[C@H](O)Cn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 23, 32, 39, 39, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 14, 14, 23, 32, 32, 117, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124986034 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986034 Building ZINC001124986673 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124986673 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/334 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O) `ZINC001124986673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124986673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124986673 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11, 21, 39, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 21, 39, 39, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/335 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O) `ZINC001124986673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124986673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124986673 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 10, 20, 39, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 20, 39, 39, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124986673 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 Building ZINC001124986673 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001124986673 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 334) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O) `ZINC001124986673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001124986673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124986673 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 11, 21, 39, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 11, 11, 21, 39, 39, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 335) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O) `ZINC001124986673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001124986673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001124986673 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCNCCN1C(=O)CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 10, 20, 39, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 10, 10, 20, 39, 39, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001124986673 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001124986673 Building ZINC001132227734 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001132227734 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/336 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O) `ZINC001132227734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001132227734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001132227734 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 25, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 5, 12, 12, 12, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/337 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O) `ZINC001132227734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001132227734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001132227734 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 10, 27, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 6, 12, 12, 12, 12, 12, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001132227734 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 Building ZINC001132227734 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001132227734 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 336) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O) `ZINC001132227734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001132227734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001132227734 none C[C@@H]1[C@H](NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 25, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 5, 12, 12, 12, 12, 12, 25, 25, 25, 25] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 337) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O) `ZINC001132227734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001132227734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001132227734 none C[C@@H]1[C@H](NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 10, 27, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 6, 12, 12, 12, 12, 12, 27, 27, 27, 27] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001132227734 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001132227734 Building ZINC001142277188 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142277188 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/338 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N1CCOCC1) `ZINC001142277188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142277188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142277188 none O=C(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 18, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 38, 38, 38, 38, 38, 18, 18, 17, 17, 4, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/339 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N1CCOCC1) `ZINC001142277188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142277188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142277188 none O=C(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 17, 16, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 35, 39, 39, 39, 39, 39, 17, 17, 16, 16, 3, 8, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142277188 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 Building ZINC001142277188 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142277188 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 338) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N1CCOCC1) `ZINC001142277188.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142277188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142277188 none O=C(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 18, 17, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 38, 38, 38, 38, 38, 18, 18, 17, 17, 4, 9, 9, 9, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 339) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N1CCOCC1) `ZINC001142277188.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142277188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142277188 none O=C(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 17, 16, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 35, 39, 39, 39, 39, 39, 17, 17, 16, 16, 3, 8, 8, 8, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142277188 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277188 Building ZINC001142277839 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142277839 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/340 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142277839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142277839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142277839 none CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 5, 6, 13, 19, 1, 5, 1, 1, 1, 10, 10, 10, 10, 15, 15, 15, 13, 13, 19, 19, 19, 19, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/341 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142277839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142277839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142277839 none CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 5, 6, 12, 18, 1, 5, 1, 1, 1, 12, 12, 12, 12, 15, 15, 15, 12, 12, 18, 18, 18, 18, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142277839 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 Building ZINC001142277839 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142277839 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 340) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142277839.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142277839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142277839 none CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 5, 6, 13, 19, 1, 5, 1, 1, 1, 10, 10, 10, 10, 15, 15, 15, 13, 13, 19, 19, 19, 19, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 341) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142277839.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142277839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142277839 none CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 5, 6, 12, 18, 1, 5, 1, 1, 1, 12, 12, 12, 12, 15, 15, 15, 12, 12, 18, 18, 18, 18, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142277839 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142277839 Building ZINC001142279070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/342 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1nccnc1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279070 none NC(=O)c1nccnc1NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 23, 23, 23, 23, 23, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 37, 37, 23, 23, 7, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/343 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1nccnc1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279070 none NC(=O)c1nccnc1NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 23, 23, 23, 23, 23, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 37, 37, 23, 23, 7, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142279070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 Building ZINC001142279070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 342) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1nccnc1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279070 none NC(=O)c1nccnc1NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 23, 23, 23, 23, 23, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 37, 37, 23, 23, 7, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 343) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1nccnc1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279070 none NC(=O)c1nccnc1NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 8, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 37, 23, 23, 23, 23, 23, 7, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 37, 37, 23, 23, 7, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142279070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279070 Building ZINC001142279405 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279405 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/344 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1nc(O)nc(O)c1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279405 none Nc1nc(O)nc(O)c1NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 12, 8, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 4, 3, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 19, 29, 29, 29, 29, 9, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 29, 29, 58, 58, 9, 11, 11, 11] 200 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/345 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1nc(O)nc(O)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279405 none Nc1nc(O)nc(O)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 12, 8, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 4, 3, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 27, 29, 29, 29, 29, 9, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 29, 29, 58, 58, 9, 11, 11, 11] 200 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142279405 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 Building ZINC001142279405 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279405 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 344) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1nc(O)nc(O)c1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279405 none Nc1nc(O)nc(O)c1NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 12, 8, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 4, 3, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 19, 29, 29, 29, 29, 9, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 29, 29, 58, 58, 9, 11, 11, 11] 200 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 345) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1nc(O)nc(O)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142279405 none Nc1nc(O)nc(O)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 12, 8, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 3, 7, 4, 3, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 27, 29, 29, 29, 29, 9, 9, 1, 9, 1, 1, 1, 11, 11, 11, 11, 29, 29, 58, 58, 9, 11, 11, 11] 200 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142279405 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142279405 Building ZINC001142280924 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142280924 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/346 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142280924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142280924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142280924 none O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 14, 14, 14, 14, 31, 31, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 14, 14, 31, 31, 31, 31, 31, 14, 14, 10, 10, 10] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/347 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142280924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142280924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142280924 none O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 15, 15, 15, 15, 15, 32, 32, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 15, 15, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142280924 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 Building ZINC001142280924 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142280924 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 346) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142280924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142280924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142280924 none O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 14, 14, 14, 14, 14, 31, 31, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 14, 14, 31, 31, 31, 31, 31, 14, 14, 10, 10, 10] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 347) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142280924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142280924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142280924 none O=C(N1CC(=O)N(C2CC2)C(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 15, 15, 15, 15, 15, 32, 32, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 15, 15, 32, 32, 32, 32, 32, 15, 15, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142280924 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280924 Building ZINC001142280928 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142280928 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/348 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142280928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142280928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142280928 none O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 15, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/349 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142280928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142280928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142280928 none O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 14, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142280928 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 Building ZINC001142280928 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142280928 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 348) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142280928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142280928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142280928 none O=C(N1CCS(=O)(=O)CC1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 15, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 349) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142280928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142280928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142280928 none O=C(N1CCS(=O)(=O)CC1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 11, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 14, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 12, 12, 12, 12, 26, 26, 26, 26, 26, 26, 26, 26, 12, 12, 12] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142280928 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142280928 Building ZINC001142281400 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281400 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/350 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281400 none O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 14, 19, 19, 19, 19, 19, 33, 19, 19, 19, 19, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 33, 33, 99, 57, 19, 19, 10, 10, 10] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/351 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281400 none O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [13, 2, 15, 21, 21, 21, 21, 21, 32, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 21, 32, 32, 96, 63, 21, 21, 10, 10, 10] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 269 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281400 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 Building ZINC001142281400 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281400 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 350) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281400 none O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 14, 19, 19, 19, 19, 19, 33, 19, 19, 19, 19, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 33, 33, 99, 57, 19, 19, 10, 10, 10] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 351) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281400 none O=C(N1CC[C@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [13, 2, 15, 21, 21, 21, 21, 21, 32, 21, 21, 21, 21, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 21, 32, 32, 96, 63, 21, 21, 10, 10, 10] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 269 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281400 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281400 Building ZINC001142281401 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281401 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/352 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281401 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 13, 21, 21, 21, 21, 21, 33, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 33, 33, 99, 63, 21, 21, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/353 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281401 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 13, 21, 21, 21, 21, 21, 32, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 32, 32, 96, 63, 21, 21, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 266 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281401 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 Building ZINC001142281401 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281401 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 352) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281401 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 13, 21, 21, 21, 21, 21, 33, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 33, 33, 99, 63, 21, 21, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 353) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281401 none O=C(N1CC[C@@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 13, 21, 21, 21, 21, 21, 32, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 32, 32, 96, 63, 21, 21, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 266 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281401 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281401 Building ZINC001142281402 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281402 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/354 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281402 none O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 10, 22, 22, 22, 22, 22, 33, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 33, 33, 99, 66, 22, 22, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 271 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/355 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281402 none O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 15, 22, 22, 22, 22, 22, 33, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 33, 33, 99, 66, 22, 22, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 270 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281402 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 Building ZINC001142281402 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281402 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 354) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281402.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281402 none O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 10, 22, 22, 22, 22, 22, 33, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 33, 33, 99, 66, 22, 22, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 271 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 355) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281402.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281402 none O=C(N1CC[C@@H](CO)[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 15, 22, 22, 22, 22, 22, 33, 22, 22, 22, 22, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 33, 33, 99, 66, 22, 22, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 270 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281402 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281402 Building ZINC001142281403 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281403 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/356 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281403 none O=C(N1CC[C@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 15, 25, 25, 25, 25, 25, 35, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 35, 35, 105, 75, 25, 25, 7, 7, 7] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 286 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/357 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/357' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281403 none O=C(N1CC[C@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 12, 23, 23, 23, 23, 23, 34, 23, 23, 23, 23, 1, 1, 1, 8, 8, 8, 8, 23, 23, 23, 23, 34, 34, 102, 69, 23, 23, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281403 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 Building ZINC001142281403 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281403 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 356) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281403 none O=C(N1CC[C@H](CO)[C@H](O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [11, 2, 15, 25, 25, 25, 25, 25, 35, 25, 25, 25, 25, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 35, 35, 105, 75, 25, 25, 7, 7, 7] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 286 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 357) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142281403 none O=C(N1CC[C@H](CO)[C@H](O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 12, 23, 23, 23, 23, 23, 34, 23, 23, 23, 23, 1, 1, 1, 8, 8, 8, 8, 23, 23, 23, 23, 34, 34, 102, 69, 23, 23, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281403 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281403 Building ZINC001142281734 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281734 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/358 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)COCC(=O)N2)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142281734 none O=C(N1CCC2(CC1)COCC(=O)N2)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 16, 32, 32, 32, 32, 26, 32, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/359 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)COCC(=O)N2)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142281734 none O=C(N1CCC2(CC1)COCC(=O)N2)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 20, 32, 32, 32, 32, 28, 32, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 31, 32, 32, 32, 32, 32, 32, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281734 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 Building ZINC001142281734 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142281734 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 358) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)COCC(=O)N2)[C@]([O-])([SiH3])c1ccco1) `ZINC001142281734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142281734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142281734 none O=C(N1CCC2(CC1)COCC(=O)N2)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 16, 32, 32, 32, 32, 26, 32, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 359) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)COCC(=O)N2)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142281734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142281734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142281734 none O=C(N1CCC2(CC1)COCC(=O)N2)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 20, 32, 32, 32, 32, 28, 32, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 31, 32, 32, 32, 32, 32, 32, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142281734 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142281734 Building ZINC001142282035 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282035 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/360 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282035 none O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 11, 21, 21, 21, 21, 21, 21, 21, 21, 34, 21, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 63, 34, 34, 102, 21, 21, 9, 9, 9] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 285 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/361 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282035 none O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 11, 24, 24, 24, 24, 24, 24, 24, 24, 36, 24, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 72, 36, 36, 108, 24, 24, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 298 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282035 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 Building ZINC001142282035 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282035 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 360) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282035 none O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [10, 2, 11, 21, 21, 21, 21, 21, 21, 21, 21, 34, 21, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 63, 34, 34, 102, 21, 21, 9, 9, 9] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 285 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 361) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282035 none O=C(N1CC[C@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 11, 24, 24, 24, 24, 24, 24, 24, 24, 36, 24, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 72, 36, 36, 108, 24, 24, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 298 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282035 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282035 Building ZINC001142282036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/362 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282036 none O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 13, 20, 20, 20, 20, 20, 20, 20, 20, 34, 20, 1, 1, 1, 8, 8, 8, 8, 20, 20, 20, 20, 60, 34, 34, 102, 20, 20, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 281 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/363 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282036 none O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 13, 21, 21, 21, 21, 21, 21, 21, 21, 33, 21, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 21, 63, 33, 33, 99, 21, 21, 10, 10, 10] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 Building ZINC001142282036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 362) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282036 none O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 13, 20, 20, 20, 20, 20, 20, 20, 20, 34, 20, 1, 1, 1, 8, 8, 8, 8, 20, 20, 20, 20, 60, 34, 34, 102, 20, 20, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 281 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 363) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282036 none O=C(N1CC[C@@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 13, 21, 21, 21, 21, 21, 21, 21, 21, 33, 21, 1, 1, 1, 10, 10, 10, 10, 21, 21, 21, 21, 63, 33, 33, 99, 21, 21, 10, 10, 10] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 278 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282036 Building ZINC001142282037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/364 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282037 none O=C(N1CC[C@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 11, 24, 24, 24, 24, 24, 24, 24, 24, 35, 24, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 72, 35, 35, 105, 24, 24, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 282 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/365 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282037 none O=C(N1CC[C@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 35, 20, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 20, 60, 35, 35, 105, 20, 20, 9, 9, 9] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 281 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 Building ZINC001142282037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 364) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282037 none O=C(N1CC[C@H](O)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 2, 11, 24, 24, 24, 24, 24, 24, 24, 24, 35, 24, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 72, 35, 35, 105, 24, 24, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 282 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 365) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282037 none O=C(N1CC[C@H](O)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 35, 20, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 20, 60, 35, 35, 105, 20, 20, 9, 9, 9] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 281 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282037 Building ZINC001142282038 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282038 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/366 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282038 none O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 12, 22, 22, 22, 22, 22, 22, 22, 22, 35, 22, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 66, 35, 35, 105, 22, 22, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 282 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/367 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282038 none O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 11, 24, 24, 24, 24, 24, 24, 24, 24, 32, 24, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 72, 32, 32, 96, 24, 24, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 260 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282038 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 Building ZINC001142282038 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282038 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 366) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282038 none O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 12, 22, 22, 22, 22, 22, 22, 22, 22, 35, 22, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 66, 35, 35, 105, 22, 22, 8, 8, 8] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 282 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 367) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142282038 none O=C(N1CC[C@@H](O)[C@@H](CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 11, 24, 24, 24, 24, 24, 24, 24, 24, 32, 24, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 72, 32, 32, 96, 24, 24, 8, 8, 8] 450 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 260 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282038 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282038 Building ZINC001142282451 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282451 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/368 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142282451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282451 none CS(=O)(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 37, 37, 10, 10, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 37, 37, 37, 28, 10, 10, 10, 6, 6, 6, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/369 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142282451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282451 none CS(=O)(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 36, 9, 9, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 9, 36, 36, 36, 24, 9, 9, 9, 7, 7, 7, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282451 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 Building ZINC001142282451 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282451 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 368) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142282451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282451 none CS(=O)(=O)NC1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 37, 37, 10, 10, 10, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 37, 37, 37, 28, 10, 10, 10, 6, 6, 6, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 369) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142282451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282451 none CS(=O)(=O)NC1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 36, 9, 9, 9, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 9, 36, 36, 36, 24, 9, 9, 9, 7, 7, 7, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282451 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282451 Building ZINC001142282470 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282470 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/370 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/371 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/372 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/372' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/373 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/373' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282470 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 Building ZINC001142282470 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282470 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 370) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 371) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 372) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 373) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282470 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 Building ZINC001142282470 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282470 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 370) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 371) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 372) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 373) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282470 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 Building ZINC001142282470 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282470 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 370) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 371) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 16, 16, 16, 3, 1, 5, 1, 1, 1, 6, 6, 6, 6, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 23, 16, 16, 6, 6, 6, 16, 16, 36, 36] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 372) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 373) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O) `ZINC001142282470.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142282470 none CN1CCN(C2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 15, 15, 15, 4, 1, 6, 1, 1, 1, 5, 5, 5, 5, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 15, 15, 5, 5, 5, 15, 15, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282470 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282470 Building ZINC001142282608 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282608 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/374 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282608 none NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 13, 40, 13, 13, 13, 6, 1, 8, 1, 1, 1, 8, 8, 8, 8, 13, 13, 13, 40, 40, 13, 13, 8, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/375 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282608 none NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 41, 16, 16, 16, 6, 1, 9, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 41, 41, 16, 16, 8, 8, 8, 16, 16, 16, 16] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282608 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 Building ZINC001142282608 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282608 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 374) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282608 none NC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 13, 40, 13, 13, 13, 6, 1, 8, 1, 1, 1, 8, 8, 8, 8, 13, 13, 13, 40, 40, 13, 13, 8, 8, 8, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 375) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282608 none NC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 41, 16, 16, 16, 6, 1, 9, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 41, 41, 16, 16, 8, 8, 8, 16, 16, 16, 16] 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282608 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282608 Building ZINC001142282609 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282609 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/376 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282609 none NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 15, 15, 15, 6, 2, 9, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 29, 29, 15, 15, 8, 8, 8, 15, 15, 15, 15] 37 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/377 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282609 none NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 15, 42, 15, 15, 15, 6, 2, 7, 1, 1, 1, 10, 10, 10, 10, 15, 15, 15, 42, 42, 15, 15, 10, 10, 10, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282609 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 Building ZINC001142282609 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282609 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 376) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282609 none NC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 15, 15, 15, 6, 2, 9, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 29, 29, 15, 15, 8, 8, 8, 15, 15, 15, 15] 37 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 377) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1) `ZINC001142282609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142282609 none NC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCO1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 15, 42, 15, 15, 15, 6, 2, 7, 1, 1, 1, 10, 10, 10, 10, 15, 15, 15, 42, 42, 15, 15, 10, 10, 10, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282609 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282609 Building ZINC001142282617 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282617 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/378 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282617 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/379 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282617 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 2, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282617 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 Building ZINC001142282617 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282617 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 378) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282617 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 379) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282617 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 2, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282617 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282617 Building ZINC001142282618 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282618 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/380 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282618 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/381 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282618 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282618 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 Building ZINC001142282618 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282618 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 380) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282618.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282618 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 381) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282618.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142282618 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282618 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282618 Building ZINC001142282665 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282665 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/382 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CNC(=O)CO2)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142282665 none O=C(N1CCC2(CC1)CNC(=O)CO2)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/383 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CNC(=O)CO2)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142282665 none O=C(N1CCC2(CC1)CNC(=O)CO2)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282665 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 Building ZINC001142282665 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282665 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 382) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CNC(=O)CO2)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142282665 none O=C(N1CCC2(CC1)CNC(=O)CO2)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 383) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)CNC(=O)CO2)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142282665 none O=C(N1CCC2(CC1)CNC(=O)CO2)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 13, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282665 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282665 Building ZINC001142282733 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282733 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/384 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142282733 none COC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 41, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 41, 41, 41, 21, 21, 7, 7, 7, 7, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/385 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142282733 none COC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 16, 34, 8, 8, 8, 8, 5, 1, 3, 1, 1, 1, 3, 3, 3, 3, 8, 8, 34, 34, 34, 16, 16, 8, 8, 8, 8, 3, 3, 3, 8, 8, 8, 8] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282733 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 Building ZINC001142282733 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282733 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 384) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282733.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142282733 none COC(=O)CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 41, 7, 7, 7, 7, 4, 1, 2, 1, 1, 1, 4, 4, 4, 4, 7, 7, 41, 41, 41, 21, 21, 7, 7, 7, 7, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 385) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282733.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142282733 none COC(=O)CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 16, 34, 8, 8, 8, 8, 5, 1, 3, 1, 1, 1, 3, 3, 3, 3, 8, 8, 34, 34, 34, 16, 16, 8, 8, 8, 8, 3, 3, 3, 8, 8, 8, 8] 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]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282733 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282733 Building ZINC001142282820 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282820 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/386 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/387 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/388 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/388' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/389 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/389' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282820 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 Building ZINC001142282820 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282820 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 386) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 387) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 388) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 389) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282820 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 Building ZINC001142282820 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282820 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 386) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 387) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 388) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 389) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282820 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 Building ZINC001142282820 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142282820 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 386) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 387) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 388) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 15, 15, 21, 38, 38, 38, 38, 38, 38, 15, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 15, 15, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 389) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282820.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142282820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282820 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 5, 13, 13, 21, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 13, 13, 7, 7, 7] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282820 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282820 Building ZINC001142282952 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282952 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/390 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142282952 none NC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 36, 25, 25, 25, 13, 1, 16, 1, 1, 1, 10, 10, 10, 10, 25, 25, 36, 36, 25, 25, 25, 25, 10, 10, 10, 25, 25, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/391 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142282952 none NC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 36, 27, 27, 27, 14, 1, 18, 1, 1, 1, 11, 11, 11, 11, 27, 27, 36, 36, 27, 27, 27, 27, 11, 11, 11, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282952 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 Building ZINC001142282952 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282952 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 390) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142282952 none NC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 36, 25, 25, 25, 13, 1, 16, 1, 1, 1, 10, 10, 10, 10, 25, 25, 36, 36, 25, 25, 25, 25, 10, 10, 10, 25, 25, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 391) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142282952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142282952 none NC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 27, 36, 27, 27, 27, 14, 1, 18, 1, 1, 1, 11, 11, 11, 11, 27, 27, 36, 36, 27, 27, 27, 27, 11, 11, 11, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142282952 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142282952 Building ZINC001142283000 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283000 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/392 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/393 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/394 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/394' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/395 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/395' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283000 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 Building ZINC001142283000 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283000 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 392) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 393) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 394) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 395) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283000 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 Building ZINC001142283000 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283000 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 392) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 393) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 394) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 395) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283000 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 Building ZINC001142283000 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283000 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 392) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 393) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 19, 34, 19, 19, 19, 11, 1, 15, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 34, 34, 34, 19, 19, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 394) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 395) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283000.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283000 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 10, 1, 11, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283000 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283000 Building ZINC001142283001 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283001 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/396 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/397 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/398 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/398' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/399 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/399' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283001 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 Building ZINC001142283001 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283001 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 396) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 397) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 398) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 399) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283001 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 Building ZINC001142283001 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283001 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 396) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 397) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 398) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 399) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283001 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 Building ZINC001142283001 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142283001 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 396) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 397) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 11, 2, 8, 1, 1, 1, 7, 7, 7, 7, 17, 17, 17, 17, 32, 32, 32, 17, 17, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 398) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 399) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C) `ZINC001142283001.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142283001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142283001 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccco2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 15, 25, 15, 15, 15, 10, 2, 7, 1, 1, 1, 9, 9, 9, 9, 15, 15, 15, 15, 25, 25, 25, 15, 15, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 40 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283001 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283001 Building ZINC001142283090 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283090 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/400 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142283090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283090 none CS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 29, 39, 39, 29, 29, 29, 8, 1, 12, 1, 1, 1, 9, 9, 9, 9, 29, 29, 39, 39, 39, 29, 29, 29, 29, 9, 9, 9, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/401 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142283090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283090 none CS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 25, 35, 35, 25, 25, 25, 8, 1, 12, 1, 1, 1, 7, 7, 7, 7, 25, 25, 35, 35, 35, 25, 25, 25, 25, 7, 7, 7, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283090 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 Building ZINC001142283090 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283090 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 400) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142283090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283090 none CS(=O)(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 29, 39, 39, 29, 29, 29, 8, 1, 12, 1, 1, 1, 9, 9, 9, 9, 29, 29, 39, 39, 39, 29, 29, 29, 29, 9, 9, 9, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 401) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142283090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283090 none CS(=O)(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 25, 35, 35, 25, 25, 25, 8, 1, 12, 1, 1, 1, 7, 7, 7, 7, 25, 25, 35, 35, 35, 25, 25, 25, 25, 7, 7, 7, 25, 25, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142283090 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142283090 Building ZINC001142284183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/402 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/403 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/404 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/404' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/405 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/405' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 Building ZINC001142284183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 402) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 403) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 404) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 405) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 Building ZINC001142284183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 402) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 403) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 404) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 405) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 Building ZINC001142284183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 402) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 403) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 18, 18, 18, 18, 18, 18, 18, 13, 2, 15, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 404) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 405) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284183 none COC(=O)[C@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 17, 32, 17, 17, 17, 17, 17, 17, 17, 12, 2, 13, 1, 1, 1, 8, 8, 8, 8, 32, 32, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284183 Building ZINC001142284184 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284184 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/406 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/407 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/408 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/408' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/409 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/409' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284184 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 Building ZINC001142284184 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284184 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 406) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 407) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 408) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 409) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284184 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 Building ZINC001142284184 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284184 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 406) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 407) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 408) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 409) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284184 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 Building ZINC001142284184 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142284184 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 406) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 407) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 14, 14, 14, 14, 14, 14, 14, 10, 1, 10, 1, 1, 1, 8, 8, 8, 8, 29, 29, 29, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8] 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 408) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 409) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284184.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142284184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142284184 none COC(=O)[C@@H]1CN(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 13, 13, 13, 13, 13, 8, 1, 9, 1, 1, 1, 7, 7, 7, 7, 29, 29, 29, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284184 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284184 Building ZINC001142284383 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284383 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/410 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncncn2)CC1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142284383 none O=C(N1CCN(c2ncncn2)CC1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 23, 23, 23, 23, 32, 32, 23, 32, 32, 23, 23, 1, 1, 1, 7, 7, 7, 7, 23, 23, 23, 23, 32, 32, 23, 23, 23, 23, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/411 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncncn2)CC1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142284383 none O=C(N1CCN(c2ncncn2)CC1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 17, 23, 23, 23, 23, 32, 32, 23, 32, 32, 23, 23, 1, 1, 1, 7, 7, 7, 7, 23, 23, 23, 23, 32, 32, 23, 23, 23, 23, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284383 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 Building ZINC001142284383 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142284383 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 410) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncncn2)CC1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142284383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142284383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142284383 none O=C(N1CCN(c2ncncn2)CC1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 17, 23, 23, 23, 23, 32, 32, 23, 32, 32, 23, 23, 1, 1, 1, 7, 7, 7, 7, 23, 23, 23, 23, 32, 32, 23, 23, 23, 23, 7, 7, 7] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 411) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(c2ncncn2)CC1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142284383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142284383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC001142284383 none O=C(N1CCN(c2ncncn2)CC1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 17, 23, 23, 23, 23, 32, 32, 23, 32, 32, 23, 23, 1, 1, 1, 7, 7, 7, 7, 23, 23, 23, 23, 32, 32, 23, 23, 23, 23, 7, 7, 7] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142284383 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142284383 Building ZINC001142285941 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142285941 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/412 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@@H](C)O) `ZINC001142285941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142285941 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 5, 15, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 15, 27, 24, 27, 29, 29, 29, 5, 8, 8, 8, 27, 27, 27, 81] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 265 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/413 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@@H](C)O) `ZINC001142285941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142285941 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 24, 4, 12, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 28, 25, 28, 24, 24, 24, 4, 8, 8, 8, 28, 28, 28, 84] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 266 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285941 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 Building ZINC001142285941 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142285941 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 412) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@@H](C)O) `ZINC001142285941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142285941 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 15, 29, 5, 15, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 15, 27, 24, 27, 29, 29, 29, 5, 8, 8, 8, 27, 27, 27, 81] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 265 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 413) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@@H](C)O) `ZINC001142285941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142285941 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 24, 4, 12, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 28, 25, 28, 24, 24, 24, 4, 8, 8, 8, 28, 28, 28, 84] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 266 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285941 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285941 Building ZINC001142285972 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285972 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/414 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/415 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/416 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/416' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/417 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/417' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285972 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 Building ZINC001142285972 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285972 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 414) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 415) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 416) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 417) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285972 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 Building ZINC001142285972 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285972 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 414) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 415) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 416) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 417) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285972 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 Building ZINC001142285972 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285972 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 414) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 415) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 38, 21, 40, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 18, 18, 3, 9, 9, 9, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 416) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 417) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285972.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285972 none CN1CCO[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 30, 17, 33, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 14, 14, 3, 8, 8, 8, 33, 33] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285972 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285972 Building ZINC001142285973 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285973 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/418 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/419 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/420 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/420' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/421 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/421' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285973 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 Building ZINC001142285973 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285973 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 418) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 419) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 420) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 421) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285973 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 Building ZINC001142285973 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285973 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 418) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 419) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 420) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 421) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285973 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 Building ZINC001142285973 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142285973 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 418) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 419) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 16, 30, 2, 2, 1, 2, 1, 1, 1, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 8, 8, 8, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 420) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 421) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142285973.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142285973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142285973 none CN1CCO[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 37, 20, 39, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 39, 39, 39, 39, 39, 39, 39, 39, 18, 18, 3, 9, 9, 9, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142285973 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142285973 Building ZINC001142286124 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286124 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/422 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286124 none O=C(N[C@@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 10, 10, 10, 10, 9, 25, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/423 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286124 none O=C(N[C@@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 10, 25, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286124 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 Building ZINC001142286124 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286124 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 422) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286124 none O=C(N[C@@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 10, 10, 10, 10, 9, 25, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 423) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286124 none O=C(N[C@@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 10, 25, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286124 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286124 Building ZINC001142286125 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286125 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/424 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286125 none O=C(N[C@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 10, 25, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/425 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286125 none O=C(N[C@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 10, 10, 10, 10, 9, 25, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286125 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 Building ZINC001142286125 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286125 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 424) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286125 none O=C(N[C@H]1SC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 11, 11, 11, 11, 10, 25, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 425) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 26 natoms 25 natoms 24 natoms 23 names: ZINC001142286125 none O=C(N[C@H]1SC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'S.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 14, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 9, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 10, 10, 10, 10, 9, 25, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286125 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286125 Building ZINC001142286146 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286146 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/426 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142286146 none CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 33, 17, 33, 33, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 17, 17, 13, 13, 3, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/427 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142286146 none CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 33, 17, 33, 33, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 41, 41, 41, 41, 17, 17, 13, 13, 3, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286146 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 Building ZINC001142286146 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286146 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 426) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142286146 none CNS(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 33, 17, 33, 33, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 17, 17, 13, 13, 3, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 427) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142286146 none CNS(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 33, 17, 33, 33, 13, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 41, 41, 41, 41, 17, 17, 13, 13, 3, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286146 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286146 Building ZINC001142286435 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286435 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/428 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286435 none O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 10, 10, 10, 10, 7, 34, 34, 34, 34, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/429 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286435 none O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 12, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 11, 11, 11, 11, 6, 33, 33, 33, 33, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286435 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 Building ZINC001142286435 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286435 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 428) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286435 none O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 10, 10, 10, 10, 7, 34, 34, 34, 34, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 429) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286435 none O=C(N[C@@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 12, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 11, 11, 11, 11, 6, 33, 33, 33, 33, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286435 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286435 Building ZINC001142286436 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286436 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/430 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286436 none O=C(N[C@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 7, 31, 31, 31, 31, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/431 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286436 none O=C(N[C@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 10, 10, 10, 10, 6, 32, 32, 32, 32, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286436 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 Building ZINC001142286436 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286436 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 430) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286436 none O=C(N[C@H]1C=CS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 7, 31, 31, 31, 31, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 431) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142286436 none O=C(N[C@H]1C=CS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.2', 'C.2', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 10, 10, 10, 10, 6, 32, 32, 32, 32, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286436 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286436 Building ZINC001142286594 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286594 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/432 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286594 none O=C(N[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/433 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286594 none O=C(N[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 11, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 11, 11, 11, 11, 7, 30, 30, 30, 30, 30, 30, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286594 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 Building ZINC001142286594 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286594 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 432) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286594 none O=C(N[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 433) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286594 none O=C(N[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 11, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 11, 11, 11, 11, 7, 30, 30, 30, 30, 30, 30, 11, 11, 11] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286594 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286594 Building ZINC001142286595 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286595 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/434 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286595 none O=C(N[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 6, 31, 31, 31, 31, 31, 31, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/435 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286595 none O=C(N[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286595 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 Building ZINC001142286595 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286595 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 434) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142286595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286595 none O=C(N[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 6, 31, 31, 31, 31, 31, 31, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 435) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142286595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142286595 none O=C(N[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 10, 10, 10] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142286595 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142286595 Building ZINC001142287175 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287175 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/436 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287175 none O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 31, 16, 22, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 5, 31, 31, 93, 22, 22, 24, 24, 9, 9, 9] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 270 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/437 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287175 none O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 28, 17, 27, 31, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 5, 28, 28, 84, 27, 27, 31, 31, 9, 9, 9] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 265 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287175 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 Building ZINC001142287175 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287175 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 436) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287175 none O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 16, 31, 16, 22, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 5, 31, 31, 93, 22, 22, 24, 24, 9, 9, 9] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 270 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 437) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287175 none O=C(N[C@@H](CO)Cc1cnc[nH]1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 17, 17, 28, 17, 27, 31, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 5, 28, 28, 84, 27, 27, 31, 31, 9, 9, 9] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 265 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287175 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287175 Building ZINC001142287297 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287297 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/438 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/439 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/440 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/440' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/441 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/441' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287297 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 Building ZINC001142287297 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287297 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 438) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 439) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 440) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 441) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287297 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 Building ZINC001142287297 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287297 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 438) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 439) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 440) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 441) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287297 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 Building ZINC001142287297 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287297 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 438) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 439) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 24, 35, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 16, 16, 4, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 440) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 441) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287297.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287297 none CN1CCOC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 25, 35, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 18, 18, 4, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 110 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287297 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287297 Building ZINC001142287298 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287298 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/442 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/443 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/444 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/444' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/445 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/445' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287298 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 Building ZINC001142287298 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287298 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 442) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 443) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 444) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 445) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287298 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 Building ZINC001142287298 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287298 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 442) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 443) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 444) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 445) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287298 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 Building ZINC001142287298 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142287298 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 442) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 443) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 33, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 33, 33, 33, 20, 20, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 444) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 445) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287298.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142287298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142287298 none CN1CCOC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 23, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 4, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287298 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287298 Building ZINC001142287322 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287322 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/446 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287322 none CCOC(=O)CN(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 7, 13, 6, 4, 6, 13, 16, 1, 4, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 23, 23, 7, 7, 13, 13, 16, 16, 16, 16, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/447 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287322 none CCOC(=O)CN(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 17, 8, 17, 6, 3, 6, 11, 13, 1, 3, 1, 1, 1, 7, 7, 7, 7, 27, 27, 27, 27, 27, 8, 8, 11, 11, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287322 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 Building ZINC001142287322 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287322 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 446) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287322 none CCOC(=O)CN(CCN)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 13, 7, 13, 6, 4, 6, 13, 16, 1, 4, 1, 1, 1, 10, 10, 10, 10, 23, 23, 23, 23, 23, 7, 7, 13, 13, 16, 16, 16, 16, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 447) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287322 none CCOC(=O)CN(CCN)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 17, 8, 17, 6, 3, 6, 11, 13, 1, 3, 1, 1, 1, 7, 7, 7, 7, 27, 27, 27, 27, 27, 8, 8, 11, 11, 13, 13, 13, 13, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287322 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287322 Building ZINC001142287445 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287445 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/448 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287445 none O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 9, 9, 9, 9, 4, 18, 18, 41, 41, 41, 41, 41, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/449 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287445 none O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 4, 18, 18, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287445 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 Building ZINC001142287445 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287445 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 448) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287445 none O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 9, 9, 9, 9, 4, 18, 18, 41, 41, 41, 41, 41, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 449) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287445 none O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 4, 18, 18, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287445 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287445 Building ZINC001142287446 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287446 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/450 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287446 none O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 3, 17, 17, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/451 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287446 none O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 9, 9, 9, 9, 4, 18, 18, 41, 41, 41, 41, 41, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287446 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 Building ZINC001142287446 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287446 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 450) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287446.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287446 none O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 23, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 9, 9, 9, 9, 3, 17, 17, 34, 34, 34, 34, 34, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 451) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287446.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287446 none O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 9, 9, 9, 9, 4, 18, 18, 41, 41, 41, 41, 41, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287446 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287446 Building ZINC001142287502 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287502 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/452 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287502 none O=C(N[C@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 7, 31, 31, 31, 31, 31, 11, 11, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/453 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287502 none O=C(N[C@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 7, 28, 28, 28, 28, 28, 11, 11, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287502 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 Building ZINC001142287502 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287502 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 452) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287502 none O=C(N[C@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 7, 31, 31, 31, 31, 31, 11, 11, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 453) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287502 none O=C(N[C@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 11, 11, 11, 11, 7, 28, 28, 28, 28, 28, 11, 11, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287502 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287502 Building ZINC001142287503 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287503 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/454 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287503 none O=C(N[C@@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 10, 10, 10, 10, 7, 32, 32, 32, 32, 32, 10, 10, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/455 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287503 none O=C(N[C@@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 7, 31, 31, 31, 31, 31, 11, 11, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287503 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 Building ZINC001142287503 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287503 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 454) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287503 none O=C(N[C@@H]1CCC(=O)NC1=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 10, 10, 10, 10, 7, 32, 32, 32, 32, 32, 10, 10, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 455) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142287503 none O=C(N[C@@H]1CCC(=O)NC1=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 11, 11, 11, 11, 7, 31, 31, 31, 31, 31, 11, 11, 11] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287503 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287503 Building ZINC001142287536 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287536 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/456 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287536 none CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 42, 15, 41, 41, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 42, 42, 15, 15, 15, 15, 3, 9, 9, 9] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/457 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287536 none CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 42, 15, 41, 41, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 42, 42, 15, 15, 15, 15, 3, 9, 9, 9] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287536 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 Building ZINC001142287536 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287536 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 456) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287536.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287536 none CN(C)S(=O)(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 42, 15, 41, 41, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 42, 42, 15, 15, 15, 15, 3, 9, 9, 9] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 457) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287536.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142287536 none CN(C)S(=O)(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 41, 42, 15, 41, 41, 15, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 42, 42, 42, 42, 42, 42, 15, 15, 15, 15, 3, 9, 9, 9] 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287536 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287536 Building ZINC001142287539 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287539 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/458 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287539 none O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 18, 18, 18, 39, 18, 40, 18, 1, 1, 1, 7, 7, 7, 7, 3, 18, 18, 18, 39, 39, 117, 40, 40, 120, 18, 18, 7, 7, 7] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 504 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/459 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287539 none O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 19, 19, 19, 39, 19, 37, 19, 1, 1, 1, 7, 7, 7, 7, 3, 19, 19, 19, 39, 39, 117, 37, 37, 111, 19, 19, 7, 7, 7] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 476 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287539 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 Building ZINC001142287539 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287539 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 458) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287539 none O=C(NC1CC(CO)(CO)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 18, 18, 18, 39, 18, 40, 18, 1, 1, 1, 7, 7, 7, 7, 3, 18, 18, 18, 39, 39, 117, 40, 40, 120, 18, 18, 7, 7, 7] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 504 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 459) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287539 none O=C(NC1CC(CO)(CO)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 12, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 5, 19, 19, 19, 39, 19, 37, 19, 1, 1, 1, 7, 7, 7, 7, 3, 19, 19, 19, 39, 39, 117, 37, 37, 111, 19, 19, 7, 7, 7] 450 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 476 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287539 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287539 Building ZINC001142287705 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287705 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/460 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CC2(COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287705 none O=C(NCCN1CC2(COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 28, 43, 43, 43, 43, 43, 38, 1, 1, 1, 7, 7, 7, 7, 3, 14, 14, 18, 18, 43, 43, 43, 43, 43, 43, 43, 43, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/461 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CC2(COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287705 none O=C(NCCN1CC2(COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 28, 42, 42, 42, 42, 42, 37, 1, 1, 1, 7, 7, 7, 7, 3, 14, 14, 18, 18, 42, 42, 42, 42, 42, 42, 42, 42, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287705 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 Building ZINC001142287705 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287705 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 460) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CC2(COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287705 none O=C(NCCN1CC2(COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 28, 43, 43, 43, 43, 43, 38, 1, 1, 1, 7, 7, 7, 7, 3, 14, 14, 18, 18, 43, 43, 43, 43, 43, 43, 43, 43, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 461) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CC2(COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142287705 none O=C(NCCN1CC2(COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 28, 42, 42, 42, 42, 42, 37, 1, 1, 1, 7, 7, 7, 7, 3, 14, 14, 18, 18, 42, 42, 42, 42, 42, 42, 42, 42, 7, 7, 7] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287705 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287705 Building ZINC001142287706 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287706 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/462 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOP(=O)(O)O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142287706 none O=C(NCCOP(=O)(O)O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 13, 11, 12, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 5, 4, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 20, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 4, 15, 15, 20, 20, 38, 38, 8, 8, 8] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/463 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOP(=O)(O)O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142287706 none O=C(NCCOP(=O)(O)O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 13, 11, 12, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 5, 4, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 20, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 4, 15, 15, 20, 20, 38, 38, 8, 8, 8] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287706 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 Building ZINC001142287706 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287706 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 462) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOP(=O)(O)O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142287706 none O=C(NCCOP(=O)(O)O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 13, 11, 12, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 5, 4, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 20, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 4, 15, 15, 20, 20, 38, 38, 8, 8, 8] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 463) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCOP(=O)(O)O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001142287706 none O=C(NCCOP(=O)(O)O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'P.3', 'O.2', 'O.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 13, 11, 12, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 5, 4, 4, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 15, 20, 38, 38, 38, 38, 1, 1, 1, 8, 8, 8, 8, 4, 15, 15, 20, 20, 38, 38, 8, 8, 8] 50 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287706 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287706 Building ZINC001142287852 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287852 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/464 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142287852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287852 none CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 34, 25, 25, 6, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 25, 34, 34, 34, 25, 25, 24, 4, 9, 9, 9, 25, 25] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/465 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142287852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287852 none CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 34, 34, 24, 24, 6, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 24, 34, 34, 34, 24, 24, 24, 4, 9, 9, 9, 24, 24] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287852 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 Building ZINC001142287852 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287852 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 464) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccco2)C1) `ZINC001142287852.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287852 none CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 25, 34, 34, 25, 25, 6, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 25, 34, 34, 34, 25, 25, 24, 4, 9, 9, 9, 25, 25] 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]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 465) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccco2)C1) `ZINC001142287852.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142287852 none CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccco2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 24, 34, 34, 24, 24, 6, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 24, 34, 34, 34, 24, 24, 24, 4, 9, 9, 9, 24, 24] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142287852 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142287852 Building ZINC001142288204 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288204 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/466 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCC(=O)O)NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001142288204 none COC(=O)[C@H](CCC(=O)O)NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 5, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 14, 25, 4, 14, 14, 20, 25, 28, 28, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 25, 26, 26, 84, 4, 7, 7, 7] 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]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/467 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCC(=O)O)NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001142288204 none COC(=O)[C@H](CCC(=O)O)NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 5, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 24, 4, 14, 14, 23, 26, 32, 32, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 24, 24, 24, 27, 27, 27, 27, 96, 4, 7, 7, 7] 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]) total number of confs: 287 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142288204 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 Building ZINC001142288204 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288204 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 466) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCC(=O)O)NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288204.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001142288204 none COC(=O)[C@H](CCC(=O)O)NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 5, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 14, 25, 4, 14, 14, 20, 25, 28, 28, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 25, 26, 26, 84, 4, 7, 7, 7] 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]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 467) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCC(=O)O)NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288204.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 36 natoms 35 natoms 34 natoms 33 names: ZINC001142288204 none COC(=O)[C@H](CCC(=O)O)NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 5, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 14, 24, 4, 14, 14, 23, 26, 32, 32, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 24, 24, 24, 27, 27, 27, 27, 96, 4, 7, 7, 7] 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]) total number of confs: 287 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142288204 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288204 Building ZINC001142288242 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288242 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/468 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1=O) `ZINC001142288242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142288242 none Cn1c(O)nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 57, 11, 10, 10, 10, 19] 108 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]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/469 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1=O) `ZINC001142288242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142288242 none Cn1c(O)nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 57, 11, 10, 10, 10, 19] 108 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]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142288242 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 Building ZINC001142288242 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288242 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 468) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1=O) `ZINC001142288242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142288242 none Cn1c(O)nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 57, 11, 10, 10, 10, 19] 108 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]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 469) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(O)nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1=O) `ZINC001142288242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142288242 none Cn1c(O)nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 12, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 19, 19, 57, 11, 10, 10, 10, 19] 108 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]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142288242 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288242 Building ZINC001142288244 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288244 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/470 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(N)N(CCCCN)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142288244 none N=C(N)N(CCCCN)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 5, 5, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 5, 7, 13, 18, 29, 38, 1, 5, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 13, 13, 18, 18, 30, 30, 39, 39, 39, 39, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/471 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(N)N(CCCCN)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142288244 none N=C(N)N(CCCCN)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 5, 5, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 5, 7, 13, 17, 28, 39, 1, 5, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 13, 13, 17, 17, 29, 29, 40, 40, 40, 40, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 209 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142288244 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 Building ZINC001142288244 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288244 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 470) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(N)N(CCCCN)C(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142288244 none N=C(N)N(CCCCN)C(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 5, 5, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 5, 7, 13, 18, 29, 38, 1, 5, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 13, 13, 18, 18, 30, 30, 39, 39, 39, 39, 7, 7, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 204 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 471) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N=C(N)N(CCCCN)C(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142288244 none N=C(N)N(CCCCN)C(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['N.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 5, 5, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 12, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [4, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 5, 7, 13, 17, 28, 39, 1, 5, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 13, 13, 17, 17, 29, 29, 40, 40, 40, 40, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 209 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142288244 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142288244 Building ZINC001142290948 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290948 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/472 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCS1(=O)=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142290948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142290948 none O=C(NCCN1CCCS1(=O)=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', '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, 5, 5, 14, 11, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 26, 38, 38, 38, 38, 38, 38, 1, 1, 1, 10, 10, 10, 10, 5, 17, 17, 22, 22, 38, 38, 38, 38, 38, 38, 10, 10, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/473 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCS1(=O)=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142290948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142290948 none O=C(NCCN1CCCS1(=O)=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', '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, 5, 5, 14, 11, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 28, 38, 38, 38, 38, 38, 38, 1, 1, 1, 10, 10, 10, 10, 5, 17, 17, 22, 22, 38, 38, 38, 38, 38, 38, 10, 10, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142290948 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 Building ZINC001142290948 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290948 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 472) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCS1(=O)=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142290948.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142290948 none O=C(NCCN1CCCS1(=O)=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', '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, 5, 5, 14, 11, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 26, 38, 38, 38, 38, 38, 38, 1, 1, 1, 10, 10, 10, 10, 5, 17, 17, 22, 22, 38, 38, 38, 38, 38, 38, 10, 10, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 473) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCS1(=O)=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142290948.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142290948 none O=C(NCCN1CCCS1(=O)=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', '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, 5, 5, 14, 11, 11, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 17, 28, 38, 38, 38, 38, 38, 38, 1, 1, 1, 10, 10, 10, 10, 5, 17, 17, 22, 22, 38, 38, 38, 38, 38, 38, 10, 10, 10] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142290948 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142290948 Building ZINC001142291037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/474 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/475 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/476 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/476' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/477 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/477' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 Building ZINC001142291037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 474) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 475) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 476) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 477) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 Building ZINC001142291037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 474) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 475) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 476) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 477) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 Building ZINC001142291037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 474) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 475) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 476) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 34, 25, 16, 16, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 25, 26, 26, 27, 40, 40, 40, 40, 34, 34, 16, 16, 16, 16, 4, 7, 7, 7, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 477) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O) `ZINC001142291037.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142291037 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccco1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 34, 22, 12, 12, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 22, 23, 23, 23, 41, 41, 41, 41, 34, 34, 12, 12, 12, 12, 3, 7, 7, 7, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291037 Building ZINC001142291238 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291238 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/478 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/479 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/480 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/480' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/481 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/481' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291238 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 Building ZINC001142291238 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291238 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 478) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 479) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 480) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 481) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291238 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 Building ZINC001142291238 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291238 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 478) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 479) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 480) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 481) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291238 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 Building ZINC001142291238 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291238 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 478) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 479) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 480) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 33, 33, 33, 31, 1, 1, 1, 9, 9, 9, 9, 4, 31, 31, 33, 33, 33, 33, 33, 31, 31, 9, 9, 9] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 481) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291238.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142291238 none O=C(N[C@H]1C[N@@](C2COC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 9, 31, 31, 31, 31, 34, 34, 34, 31, 1, 1, 1, 8, 8, 8, 8, 4, 31, 31, 34, 34, 34, 34, 34, 31, 31, 8, 8, 8] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291238 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291238 Building ZINC001142291241 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142291241 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/482 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(N)=O) `ZINC001142291241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142291241 none COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 10, 6, 4, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 6, 14, 14, 37, 37, 37, 17, 17, 10, 10, 4, 7, 7, 7, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/483 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(N)=O) `ZINC001142291241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142291241 none COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 21, 39, 13, 8, 5, 8, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 8, 15, 15, 39, 39, 39, 21, 21, 13, 13, 5, 6, 6, 6, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291241 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 Building ZINC001142291241 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142291241 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 482) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(N)=O) `ZINC001142291241.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142291241 none COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 10, 6, 4, 6, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 6, 14, 14, 37, 37, 37, 17, 17, 10, 10, 4, 7, 7, 7, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 483) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(N)=O) `ZINC001142291241.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142291241 none COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 21, 39, 13, 8, 5, 8, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 8, 15, 15, 39, 39, 39, 21, 21, 13, 13, 5, 6, 6, 6, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142291241 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142291241 Building ZINC001142682201 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142682201 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/484 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142682201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142682201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142682201 none CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 18, 5, 7, 13, 21, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 18, 18, 18, 13, 13, 21, 21, 21, 21, 4, 4, 1, 4, 4] 34 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/485 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142682201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142682201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142682201 none CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 5, 6, 14, 21, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 17, 17, 17, 14, 14, 21, 21, 21, 21, 3, 3, 1, 3, 3] 32 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142682201 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 Building ZINC001142682201 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142682201 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 484) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142682201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142682201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142682201 none CS(=O)(=O)N(CCN)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [18, 7, 18, 18, 5, 7, 13, 21, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 18, 18, 18, 13, 13, 21, 21, 21, 21, 4, 4, 1, 4, 4] 34 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 485) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142682201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142682201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142682201 none CS(=O)(=O)N(CCN)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 10, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 17, 17, 5, 6, 14, 21, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 17, 17, 17, 14, 14, 21, 21, 21, 21, 3, 3, 1, 3, 3] 32 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142682201 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142682201 Building ZINC001142686766 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686766 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/486 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142686766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686766 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 2, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 1, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/487 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142686766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686766 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 2, 28, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 5, 5, 1, 5, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142686766 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 Building ZINC001142686766 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686766 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 486) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142686766.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686766 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 2, 27, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 1, 5, 5, 1, 5, 5, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 487) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142686766.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686766 none O=C(N1CCN2C(=O)COC[C@H]2C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 2, 28, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 5, 5, 1, 5, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142686766 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686766 Building ZINC001142686767 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686767 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/488 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142686767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686767 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 2, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 5, 5, 1, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/489 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142686767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686767 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 2, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 1, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 2, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142686767 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 Building ZINC001142686767 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142686767 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 488) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142686767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142686767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686767 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 2, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 5, 5, 1, 5, 5, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 1, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 489) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142686767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142686767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001142686767 none O=C(N1CCN2C(=O)COC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 2, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 5, 5, 1, 5, 5, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 2, 5, 5] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142686767 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142686767 Building ZINC001142687039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142687039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/490 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/491 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/492 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/492' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/493 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/493' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142687039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 Building ZINC001142687039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142687039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 490) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 491) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 492) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 493) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142687039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 Building ZINC001142687039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142687039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 490) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 491) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 492) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 493) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142687039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 Building ZINC001142687039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142687039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 490) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 491) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 492) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 28, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 493) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142687039.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142687039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142687039 none O=C(N1CC(N2CCNC(=O)C2)C1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 6, 19, 19, 31, 49, 49, 49, 49, 49, 49, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 49, 49, 49, 49, 49, 49, 49, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142687039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142687039 Building ZINC001142691509 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691509 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/494 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691509 none O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 12, 5, 7, 12, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 1350 conformations in input total number of sets (complete confs): 1350 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 8, 27, 27, 27, 27, 27, 39, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 1, 5, 5, 5, 27, 27, 39, 39, 117, 81, 81, 5, 5, 1, 5, 5] 1350 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 425 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/495 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691509 none O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 12, 5, 7, 12, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 1350 conformations in input total number of sets (complete confs): 1350 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 10, 29, 29, 29, 29, 29, 44, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 1, 5, 5, 6, 29, 29, 44, 44, 132, 87, 87, 5, 5, 2, 5, 5] 1350 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]) total number of confs: 469 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691509 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 Building ZINC001142691509 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691509 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 494) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691509 none O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 12, 5, 7, 12, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 1350 conformations in input total number of sets (complete confs): 1350 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 8, 27, 27, 27, 27, 27, 39, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 1, 5, 5, 5, 27, 27, 39, 39, 117, 81, 81, 5, 5, 1, 5, 5] 1350 rigid atoms, others: [1, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 425 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 495) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691509 none O=C(N[C@@H]1C[C@H](CO)[C@@H](O)[C@H]1O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 12, 5, 7, 12, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 3 hydrogens need rotated 1350 conformations in input total number of sets (complete confs): 1350 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 10, 29, 29, 29, 29, 29, 44, 29, 29, 29, 29, 29, 29, 1, 1, 1, 5, 5, 1, 5, 5, 6, 29, 29, 44, 44, 132, 87, 87, 5, 5, 2, 5, 5] 1350 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]) total number of confs: 469 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691509 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691509 Building ZINC001142691706 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691706 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/496 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC001142691706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142691706 none CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 25, 44, 44, 25, 25, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 25, 44, 44, 44, 25, 25, 25, 4, 3, 3, 1, 3, 3, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/497 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC001142691706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142691706 none CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 29, 46, 46, 29, 29, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 29, 46, 46, 46, 29, 29, 28, 4, 3, 3, 1, 3, 3, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691706 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 Building ZINC001142691706 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691706 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 496) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC001142691706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142691706 none CS(=O)(=O)N1CC(NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 25, 44, 44, 25, 25, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 25, 44, 44, 44, 25, 25, 25, 4, 3, 3, 1, 3, 3, 25, 25] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 497) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC001142691706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142691706 none CS(=O)(=O)N1CC(NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 29, 46, 46, 29, 29, 6, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 29, 46, 46, 46, 29, 29, 28, 4, 3, 3, 1, 3, 3, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691706 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691706 Building ZINC001142691926 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691926 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/498 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(N)=O) `ZINC001142691926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691926 none COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 23, 50, 14, 7, 3, 7, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 7, 14, 14, 50, 50, 50, 23, 23, 14, 14, 3, 3, 3, 1, 3, 3, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/499 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(N)=O) `ZINC001142691926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691926 none COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 22, 45, 15, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 6, 10, 10, 45, 45, 45, 22, 22, 15, 15, 3, 3, 3, 1, 3, 3, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691926 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 Building ZINC001142691926 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691926 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 498) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(N)=O) `ZINC001142691926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691926 none COC(=O)CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccccc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 23, 50, 14, 7, 3, 7, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 7, 14, 14, 50, 50, 50, 23, 23, 14, 14, 3, 3, 3, 1, 3, 3, 14, 14] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 499) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(N)=O) `ZINC001142691926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142691926 none COC(=O)CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccccc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 22, 45, 15, 6, 3, 6, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 6, 10, 10, 45, 45, 45, 22, 22, 15, 15, 3, 3, 3, 1, 3, 3, 10, 10] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691926 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691926 Building ZINC001142691928 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691928 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/500 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/501 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/502 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/502' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/503 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/503' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691928 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 Building ZINC001142691928 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691928 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 500) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 501) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 502) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 503) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691928 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 Building ZINC001142691928 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691928 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 500) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 501) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 502) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 503) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691928 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 Building ZINC001142691928 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142691928 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 500) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 501) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 502) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 41, 33, 16, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 33, 36, 36, 36, 47, 47, 47, 47, 41, 41, 16, 16, 14, 14, 2, 3, 3, 1, 3, 3, 36] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 503) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O) `ZINC001142691928.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142691928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142691928 none NCCN(CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1)N(O)N=O NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.3', 'N.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 8, 12, 8, 11, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 45, 37, 21, 16, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 37, 42, 42, 42, 47, 47, 47, 47, 45, 45, 21, 21, 16, 16, 3, 3, 3, 1, 3, 3, 42] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691928 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691928 Building ZINC001142691932 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691932 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/504 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142691932 none COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 46, 48, 24, 24, 13, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 46, 46, 24, 13, 13, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/505 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142691932 none COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 46, 48, 24, 24, 13, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 46, 46, 24, 13, 13, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691932 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 Building ZINC001142691932 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142691932 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 504) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142691932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142691932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142691932 none COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 46, 48, 24, 24, 13, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 46, 46, 24, 13, 13, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 505) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142691932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142691932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142691932 none COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 46, 48, 24, 24, 13, 24, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 46, 46, 24, 13, 13, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142691932 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142691932 Building ZINC001142692003 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142692003 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/506 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142692003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142692003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692003 none O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 32, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 3, 3, 4, 21, 21, 42, 42, 42, 42, 42, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/507 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142692003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142692003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692003 none O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 29, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 1, 3, 3, 5, 21, 21, 45, 45, 45, 45, 45, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142692003 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 Building ZINC001142692003 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142692003 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 506) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142692003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142692003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692003 none O=C(NC[C@@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 32, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 3, 3, 4, 21, 21, 42, 42, 42, 42, 42, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 507) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142692003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142692003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692003 none O=C(NC[C@@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 29, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 1, 3, 3, 5, 21, 21, 45, 45, 45, 45, 45, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142692003 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692003 Building ZINC001142692004 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142692004 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/508 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142692004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142692004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692004 none O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 29, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 1, 3, 3, 5, 21, 21, 45, 45, 45, 45, 45, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/509 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142692004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142692004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692004 none O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 30, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 3, 3, 4, 21, 21, 42, 42, 42, 42, 42, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142692004 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 Building ZINC001142692004 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142692004 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 508) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142692004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142692004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692004 none O=C(NC[C@H]1CNC(=O)CO1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 29, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 3, 3, 1, 3, 3, 5, 21, 21, 45, 45, 45, 45, 45, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 509) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142692004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142692004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142692004 none O=C(NC[C@H]1CNC(=O)CO1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 6, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 30, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 3, 3, 4, 21, 21, 42, 42, 42, 42, 42, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142692004 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142692004 Building ZINC001142693679 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142693679 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/510 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001142693679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142693679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693679 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 18, 25, 25, 24, 25, 38, 39, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/511 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001142693679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142693679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693679 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 17, 23, 23, 20, 23, 34, 35, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142693679 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 Building ZINC001142693679 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142693679 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 510) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001142693679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142693679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693679 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 18, 25, 25, 24, 25, 38, 39, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 511) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001142693679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142693679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693679 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 17, 23, 23, 20, 23, 34, 35, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 152 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142693679 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693679 Building ZINC001142693680 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142693680 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/512 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001142693680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142693680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693680 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 17, 21, 21, 21, 21, 36, 38, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/513 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001142693680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142693680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693680 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 16, 18, 18, 18, 18, 36, 39, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142693680 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 Building ZINC001142693680 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142693680 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 512) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001142693680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142693680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693680 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 17, 21, 21, 21, 21, 36, 38, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 135 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 513) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001142693680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142693680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142693680 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 16, 18, 18, 18, 18, 36, 39, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142693680 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142693680 Building ZINC001142695133 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695133 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/514 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1) `ZINC001142695133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695133 none C[C@@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 37, 37, 37, 37, 37, 46, 50, 50, 50, 50, 50, 1, 1, 1, 8, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/515 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1) `ZINC001142695133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695133 none C[C@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 36, 36, 36, 36, 36, 44, 50, 50, 50, 50, 50, 1, 1, 1, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695133 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 Building ZINC001142695133 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695133 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 514) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1) `ZINC001142695133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695133 none C[C@@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 37, 37, 37, 37, 37, 46, 50, 50, 50, 50, 50, 1, 1, 1, 8, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 515) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1) `ZINC001142695133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695133 none C[C@]([O-])([SiH3])C(=O)Nc1nccnc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 36, 36, 36, 36, 36, 44, 50, 50, 50, 50, 50, 1, 1, 1, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 81 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695133 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695133 Building ZINC001142695283 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695283 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/516 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1) `ZINC001142695283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142695283 none C[C@@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 11, 1, 1, 1, 3, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/517 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1) `ZINC001142695283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142695283 none C[C@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 11, 1, 1, 1, 3, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695283 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 Building ZINC001142695283 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695283 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 516) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1) `ZINC001142695283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142695283 none C[C@@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 11, 1, 1, 1, 3, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 517) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1) `ZINC001142695283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142695283 none C[C@]([O-])([SiH3])C(=O)Nc1cnn(CCN2CCOCC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 10, 5, 5, 12, 5, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 33, 33, 50, 50, 50, 50, 50, 11, 1, 1, 1, 3, 11, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695283 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695283 Building ZINC001142695355 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695355 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/518 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142695355 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 19, 47, 19, 19, 19, 19, 19, 27, 27, 6, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 27, 27, 6, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/519 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142695355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142695355 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 46, 19, 46, 19, 19, 19, 19, 19, 28, 28, 6, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 28, 28, 6, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695355 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 Building ZINC001142695355 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695355 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 518) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142695355 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 47, 19, 47, 19, 19, 19, 19, 19, 27, 27, 6, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 27, 27, 6, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 519) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142695355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142695355 none CCOC(=O)c1snc(C(N)=O)c1NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'N.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 8, 1, 1, 8, 11, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 46, 19, 46, 19, 19, 19, 19, 19, 28, 28, 6, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 28, 28, 6, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695355 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695355 Building ZINC001142695420 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695420 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/520 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/521 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 16, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/522 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/522' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/523 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/523' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 8, 15, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 5, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695420 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 Building ZINC001142695420 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695420 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 520) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 521) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 16, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 522) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 523) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 8, 15, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 5, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695420 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 Building ZINC001142695420 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695420 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 520) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 521) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 16, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 522) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 523) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 8, 15, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 5, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695420 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 Building ZINC001142695420 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695420 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 520) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 521) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 16, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 522) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 9, 9, 17, 50, 50, 50, 50, 50, 50, 9, 9, 9, 1, 1, 1, 5, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 523) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1) `ZINC001142695420.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695420 none C[C@]([O-])([SiH3])C(=O)Nc1cc([N@]2CC[N@@](C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.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, 8, 1, 1, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 8, 8, 15, 50, 50, 50, 50, 50, 50, 8, 8, 8, 1, 1, 1, 5, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695420 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695420 Building ZINC001142695484 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695484 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/524 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1) `ZINC001142695484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695484 none C[C@@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 21, 50, 50, 50, 50, 50, 13, 1, 1, 1, 7, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/525 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1) `ZINC001142695484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695484 none C[C@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 20, 50, 50, 50, 50, 50, 13, 1, 1, 1, 7, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695484 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 Building ZINC001142695484 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695484 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 524) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1) `ZINC001142695484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695484 none C[C@@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 21, 50, 50, 50, 50, 50, 13, 1, 1, 1, 7, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 87 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 525) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1) `ZINC001142695484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142695484 none C[C@]([O-])([SiH3])C(=O)Nc1cncc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 20, 50, 50, 50, 50, 50, 13, 1, 1, 1, 7, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 86 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695484 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695484 Building ZINC001142695524 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695524 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/526 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 25, 25, 9, 32, 50, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/527 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 9, 29, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/528 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/528' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 11, 31, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/529 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/529' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 20, 20, 9, 27, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 6, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695524 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 Building ZINC001142695524 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695524 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 526) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 25, 25, 9, 32, 50, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 527) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 9, 29, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 528) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 11, 31, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 529) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 20, 20, 9, 27, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 6, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695524 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 Building ZINC001142695524 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695524 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 526) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 25, 25, 9, 32, 50, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 527) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 9, 29, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 528) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 11, 31, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 529) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 20, 20, 9, 27, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 6, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695524 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 Building ZINC001142695524 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695524 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 526) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 25, 25, 9, 32, 50, 50, 50, 50, 50, 50, 25, 25, 1, 1, 1, 6, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 527) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1) `ZINC001142695524.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 9, 29, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 528) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 23, 23, 11, 31, 50, 50, 50, 50, 50, 50, 23, 23, 1, 1, 1, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 529) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1) `ZINC001142695524.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695524 none C[C@]([O-])([SiH3])C(=O)Nc1cnc([N@]2CC[N@@](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 8, 5, 5, 10, 5, 5, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 20, 20, 9, 27, 50, 50, 50, 50, 50, 50, 20, 20, 1, 1, 1, 6, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695524 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695524 Building ZINC001142695606 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695606 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/530 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142695606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695606 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 8, 8, 50, 50, 50, 50, 49, 49, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 171 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/531 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142695606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695606 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 7, 7, 50, 50, 50, 50, 46, 46, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 178 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695606 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 Building ZINC001142695606 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695606 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 530) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142695606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695606 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 20, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 8, 8, 50, 50, 50, 50, 49, 49, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 171 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 531) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142695606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695606 none CNC(=O)CO[C@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 18, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 5, 1, 1, 1, 7, 7, 50, 50, 50, 50, 46, 46, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 178 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695606 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695606 Building ZINC001142695607 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695607 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/532 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142695607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695607 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 2, 7, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/533 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142695607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695607 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 21, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 7, 1, 1, 1, 9, 9, 50, 50, 50, 50, 48, 48, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695607 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 Building ZINC001142695607 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695607 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 532) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142695607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695607 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 2, 7, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 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, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 533) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142695607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695607 none CNC(=O)CO[C@@H]1COC2(C1)CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 7, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 48, 50, 21, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 7, 1, 1, 1, 9, 9, 50, 50, 50, 50, 48, 48, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 170 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695607 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695607 Building ZINC001142695608 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695608 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/534 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001142695608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695608 none C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 12, 14, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/535 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001142695608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695608 none C[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 11, 14, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695608 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 Building ZINC001142695608 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695608 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 534) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001142695608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695608 none C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 12, 14, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 535) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001142695608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695608 none C[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 11, 14, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 19, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695608 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695608 Building ZINC001142695611 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695611 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/536 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2) `ZINC001142695611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695611 none CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 37, 37, 37, 37, 34, 14, 1, 21, 1, 1, 1, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 37, 32, 37, 37] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/537 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2) `ZINC001142695611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695611 none CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 38, 38, 38, 38, 37, 15, 1, 24, 1, 1, 1, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 38, 34, 38, 38] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695611 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 Building ZINC001142695611 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695611 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 536) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2) `ZINC001142695611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695611 none CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 37, 37, 37, 37, 34, 14, 1, 21, 1, 1, 1, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 37, 32, 37, 37] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 537) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2) `ZINC001142695611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695611 none CC(=O)N1CCC[C@@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 38, 38, 38, 38, 37, 15, 1, 24, 1, 1, 1, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 38, 34, 38, 38] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695611 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695611 Building ZINC001142695612 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695612 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/538 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2) `ZINC001142695612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695612 none CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 38, 38, 38, 38, 34, 12, 2, 19, 1, 1, 1, 36, 38, 38, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 1, 1, 1, 38, 38, 38, 38] 50 rigid atoms, others: [32, 33, 34, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/539 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2) `ZINC001142695612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695612 none CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 40, 40, 40, 40, 34, 11, 2, 19, 1, 1, 1, 38, 40, 40, 50, 50, 50, 40, 40, 40, 40, 40, 40, 40, 40, 40, 38, 1, 1, 1, 40, 40, 40, 40] 50 rigid atoms, others: [32, 33, 34, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695612 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 Building ZINC001142695612 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695612 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 538) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2) `ZINC001142695612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695612 none CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 38, 38, 38, 38, 34, 12, 2, 19, 1, 1, 1, 36, 38, 38, 50, 50, 50, 38, 38, 38, 38, 38, 38, 38, 38, 36, 38, 1, 1, 1, 38, 38, 38, 38] 50 rigid atoms, others: [32, 33, 34, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 539) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2) `ZINC001142695612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695612 none CC(=O)N1CCC[C@]2(C1)CN(C(=O)[C@](C)([O-])[SiH3])CCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 40, 40, 40, 40, 34, 11, 2, 19, 1, 1, 1, 38, 40, 40, 50, 50, 50, 40, 40, 40, 40, 40, 40, 40, 40, 40, 38, 1, 1, 1, 40, 40, 40, 40] 50 rigid atoms, others: [32, 33, 34, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695612 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695612 Building ZINC001142695631 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695631 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/540 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142695631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142695631 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 1, 16, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 32, 32, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 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, 42, 43]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/541 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142695631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142695631 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 33, 33, 15, 15, 15, 15, 15, 15, 1, 1, 1, 15, 15] 50 rigid atoms, others: [39, 40, 41, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 169 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695631 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 Building ZINC001142695631 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695631 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 540) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142695631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142695631 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 1, 16, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 32, 32, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 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, 42, 43]) total number of confs: 159 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 541) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142695631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142695631 none CN(C)C(=O)NC[C@H]1OC[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 33, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 2, 14, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 33, 33, 15, 15, 15, 15, 15, 15, 1, 1, 1, 15, 15] 50 rigid atoms, others: [39, 40, 41, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43]) total number of confs: 169 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695631 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695631 Building ZINC001142695636 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695636 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/542 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/543 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/544 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/544' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/545 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/545' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695636 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 Building ZINC001142695636 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695636 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 542) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 543) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 544) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 545) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695636 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 Building ZINC001142695636 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695636 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 542) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 543) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 544) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 545) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695636 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 Building ZINC001142695636 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695636 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 542) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 543) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 544) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 32, 50, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 32, 32, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 545) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142695636.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695636 none CN(C)CCN1CC[C@@H]2[C@@H]1CCN2C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [50, 37, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 32, 32, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695636 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695636 Building ZINC001142695656 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695656 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/546 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@H]21) `ZINC001142695656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695656 none CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 17, 42, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 2, 11, 1, 1, 1, 17, 17, 17, 42, 42, 42, 42, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 42 rigid atoms, others: [34, 35, 36, 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, 37, 38]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/547 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]21) `ZINC001142695656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695656 none CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 15, 40, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 2, 11, 1, 1, 1, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 15, 15] 40 rigid atoms, others: [34, 35, 36, 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, 37, 38]) total number of confs: 109 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695656 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 Building ZINC001142695656 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695656 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 546) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@H]21) `ZINC001142695656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695656 none CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 17, 42, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 2, 11, 1, 1, 1, 17, 17, 17, 42, 42, 42, 42, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 42 rigid atoms, others: [34, 35, 36, 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, 37, 38]) total number of confs: 113 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 547) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]21) `ZINC001142695656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695656 none CNC(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 15, 40, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 2, 11, 1, 1, 1, 15, 15, 15, 40, 40, 40, 40, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 15, 15] 40 rigid atoms, others: [34, 35, 36, 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, 37, 38]) total number of confs: 109 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695656 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695656 Building ZINC001142695700 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695700 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/548 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/549 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/550 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/550' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/551 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/551' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695700 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 Building ZINC001142695700 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695700 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 548) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 549) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 550) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 551) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695700 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 Building ZINC001142695700 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695700 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 548) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 549) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 550) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 551) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695700 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 Building ZINC001142695700 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142695700 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 548) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 549) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 550) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 551) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001142695700.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142695700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695700 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695700 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695700 Building ZINC001142695703 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695703 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/552 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142695703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142695703 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 9, 45, 9, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17, 28, 29, 30] 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, 31, 32]) total number of confs: 118 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/553 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142695703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142695703 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 9, 45, 9, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17, 28, 29, 30] 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, 31, 32]) total number of confs: 118 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695703 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 Building ZINC001142695703 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695703 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 552) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142695703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142695703 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 9, 45, 9, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17, 28, 29, 30] 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, 31, 32]) total number of confs: 118 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 553) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142695703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142695703 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 9, 45, 9, 9, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 9, 50, 50, 50, 50, 50, 9, 9, 9, 9, 1, 1, 1, 9, 9] 50 rigid atoms, others: [13, 15, 16, 17, 28, 29, 30] 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, 31, 32]) total number of confs: 118 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695703 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695703 Building ZINC001142695722 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695722 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/554 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2C1=O) `ZINC001142695722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695722 none COCCN1CCO[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 14, 14, 14, 14, 14, 14, 14, 14, 12, 2, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 31, 31, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 240 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/555 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2C1=O) `ZINC001142695722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695722 none COCCN1CCO[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 11, 2, 13, 1, 1, 1, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 32, 32, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 230 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695722 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 Building ZINC001142695722 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695722 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 554) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2C1=O) `ZINC001142695722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695722 none COCCN1CCO[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 14, 14, 14, 14, 14, 14, 14, 14, 12, 2, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 31, 31, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 240 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 555) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2C1=O) `ZINC001142695722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142695722 none COCCN1CCO[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2C1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 14, 14, 14, 14, 14, 14, 14, 14, 11, 2, 13, 1, 1, 1, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50, 50, 32, 32, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 230 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695722 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695722 Building ZINC001142695879 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695879 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/556 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21) `ZINC001142695879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695879 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 42, 46, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/557 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21) `ZINC001142695879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695879 none C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 44, 46, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695879 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 Building ZINC001142695879 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695879 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 556) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21) `ZINC001142695879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695879 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 10, 12, 12, 12, 12, 12, 12, 12, 12, 42, 46, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 557) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21) `ZINC001142695879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142695879 none C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@@H](C(=O)N3CCCO3)CC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 44, 46, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695879 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695879 Building ZINC001142695920 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695920 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/558 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21) `ZINC001142695920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142695920 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 33, 50, 50, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 23, 33, 33, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/559 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21) `ZINC001142695920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142695920 none C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 50, 50, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 23, 36, 36, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695920 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 Building ZINC001142695920 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695920 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 558) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21) `ZINC001142695920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142695920 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 33, 50, 50, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 23, 33, 33, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 559) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21) `ZINC001142695920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142695920 none C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2O[C@H](C(=O)NCC3CC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 36, 50, 50, 6, 6, 6, 1, 1, 1, 6, 6, 6, 6, 23, 36, 36, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695920 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695920 Building ZINC001142695931 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695931 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/560 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1) `ZINC001142695931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695931 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 1, 1, 1, 14] 14 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 27 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/561 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/561' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1) `ZINC001142695931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695931 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 1, 1, 1, 15] 15 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 28 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695931 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 Building ZINC001142695931 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695931 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 560) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1) `ZINC001142695931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695931 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 6, 6, 1, 1, 1, 14] 14 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 27 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 561) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1) `ZINC001142695931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142695931 none Cn1cc(N2C(=O)C[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 11, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 1, 1, 1, 15] 15 rigid atoms, others: [32, 33, 34, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 28 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695931 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695931 Building ZINC001142695961 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695961 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/562 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1) `ZINC001142695961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695961 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 8, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 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, 38]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/563 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1) `ZINC001142695961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695961 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 8, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 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, 38]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695961 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 Building ZINC001142695961 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142695961 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 562) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1) `ZINC001142695961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142695961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695961 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 8, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 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, 38]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 563) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1) `ZINC001142695961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142695961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142695961 none Cn1cc(C(=O)N2CC[C@@H]3[C@@H]2CCN3C(=O)[C@@](C)([O-])[SiH3])cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 8, 27, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 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, 38]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142695961 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142695961 Building ZINC001142696024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/564 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/565 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/566 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/566' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/567 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/567' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 Building ZINC001142696024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 564) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 565) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 566) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 567) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 Building ZINC001142696024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 564) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 565) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 566) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 567) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 Building ZINC001142696024 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696024 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 564) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 565) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 566) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 43, 22, 22, 22, 22, 22, 22, 22, 22, 15, 1, 18, 1, 1, 1, 22, 22, 22, 22, 22, 50, 50, 50, 49, 49, 43, 43, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 567) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1) `ZINC001142696024.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696024 none COCCN1CCO[C@@H]2CN(C(=O)[C@@](C)([O-])[SiH3])CC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 20, 20, 20, 20, 20, 20, 20, 20, 14, 1, 15, 1, 1, 1, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 41, 41, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [35, 36, 37, 12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696024 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696024 Building ZINC001142696039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/568 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142696039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696039 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 14, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 43, 43, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14] 50 rigid atoms, others: [35, 36, 37, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 189 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/569 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142696039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696039 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 14, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14] 50 rigid atoms, others: [35, 36, 37, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 187 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 Building ZINC001142696039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 568) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142696039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696039 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 14, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 43, 43, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14] 50 rigid atoms, others: [35, 36, 37, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 189 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 569) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142696039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696039 none CC(=O)N(C)Cc1nnc2n1CCCN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 8, 8, 1, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 50, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 1, 14, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 45, 45, 14, 14, 14, 14, 14, 14, 1, 1, 1, 14, 14] 50 rigid atoms, others: [35, 36, 37, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39]) total number of confs: 187 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696039 Building ZINC001142696057 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696057 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/570 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/571 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/572 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/572' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/573 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/573' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696057 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 Building ZINC001142696057 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696057 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 570) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 571) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 572) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 573) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696057 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 Building ZINC001142696057 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696057 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 570) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 571) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 572) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 573) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696057 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 Building ZINC001142696057 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696057 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 570) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 571) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 572) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 45, 45, 21, 45, 45, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 45, 21, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 573) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001142696057.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696057 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 45, 45, 20, 45, 45, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 45, 20, 45] 45 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696057 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696057 Building ZINC001142696109 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696109 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/574 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696109 none Cn1cc(N2C[C@@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 1, 12, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/575 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696109 none Cn1cc(N2C[C@@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 4, 1, 12, 1, 1, 1, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 1, 1, 1, 27, 27, 27, 27, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696109 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 Building ZINC001142696109 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696109 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 574) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696109 none Cn1cc(N2C[C@@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 1, 12, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 575) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696109 none Cn1cc(N2C[C@@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 4, 1, 12, 1, 1, 1, 27, 27, 27, 27, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 1, 1, 1, 27, 27, 27, 27, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696109 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696109 Building ZINC001142696111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/576 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696111 none Cn1cc(N2C[C@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 1, 8, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/577 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696111 none Cn1cc(N2C[C@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 1, 10, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 Building ZINC001142696111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 576) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696111 none Cn1cc(N2C[C@]3(CCN(C(=O)[C@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 1, 8, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 577) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1) `ZINC001142696111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696111 none Cn1cc(N2C[C@]3(CCN(C(=O)[C@@](C)([O-])[SiH3])C3)CC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 26, 26, 26, 26, 26, 4, 1, 10, 1, 1, 1, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 1, 1, 1, 26, 26, 26, 26, 50] 50 rigid atoms, others: [32, 33, 10, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696111 Building ZINC001142696113 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696113 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/578 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1) `ZINC001142696113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696113 none C[C@@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 14, 14, 37, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14, 37, 37, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 155 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/579 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1) `ZINC001142696113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696113 none C[C@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 14, 14, 36, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14, 36, 36, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 155 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696113 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 Building ZINC001142696113 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696113 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 578) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1) `ZINC001142696113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696113 none C[C@@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 11, 14, 14, 14, 14, 14, 14, 37, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14, 37, 37, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 155 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 579) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1) `ZINC001142696113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696113 none C[C@]([O-])([SiH3])C(=O)N1CCCn2c(Cn3cccn3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 8, 1, 1, 1, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 10, 14, 14, 14, 14, 14, 14, 36, 50, 50, 50, 50, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14, 36, 36, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 155 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696113 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696113 Building ZINC001142696168 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696168 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/580 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1) `ZINC001142696168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696168 none C[C@@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 8, 31, 44, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/581 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1) `ZINC001142696168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696168 none C[C@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 29, 42, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696168 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 Building ZINC001142696168 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696168 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 580) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1) `ZINC001142696168.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696168 none C[C@@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 8, 31, 44, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 581) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1) `ZINC001142696168.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696168 none C[C@]([O-])([SiH3])C(=O)N1Cc2[nH]nc(C(=O)N3CCOCC3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 29, 42, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696168 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696168 Building ZINC001142696196 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696196 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/582 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142696196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696196 none CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 43, 12, 5, 1, 9, 1, 1, 1, 12, 29, 29, 29, 29, 29, 33, 33, 43, 43, 43, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 220 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/583 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142696196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696196 none CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 12, 12, 12, 12, 12, 12, 12, 12, 32, 43, 12, 5, 1, 9, 1, 1, 1, 12, 29, 29, 29, 29, 29, 32, 32, 43, 43, 43, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 222 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696196 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 Building ZINC001142696196 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696196 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 582) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142696196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696196 none CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 43, 12, 5, 1, 9, 1, 1, 1, 12, 29, 29, 29, 29, 29, 33, 33, 43, 43, 43, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 220 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 583) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142696196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696196 none CCn1nnc2c1[C@@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 12, 12, 12, 12, 12, 12, 12, 12, 32, 43, 12, 5, 1, 9, 1, 1, 1, 12, 29, 29, 29, 29, 29, 32, 32, 43, 43, 43, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 222 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696196 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696196 Building ZINC001142696197 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696197 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/584 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142696197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696197 none CCn1nnc2c1[C@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 42, 12, 5, 1, 9, 1, 1, 1, 12, 29, 29, 29, 29, 29, 31, 31, 42, 42, 42, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 219 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/585 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142696197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696197 none CCn1nnc2c1[C@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 43, 12, 5, 1, 9, 1, 1, 1, 12, 30, 30, 30, 30, 30, 33, 33, 43, 43, 43, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 223 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696197 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 Building ZINC001142696197 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696197 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 584) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2) `ZINC001142696197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696197 none CCn1nnc2c1[C@H](COC)CN(C(=O)[C@@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 42, 12, 5, 1, 9, 1, 1, 1, 12, 29, 29, 29, 29, 29, 31, 31, 42, 42, 42, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 219 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 585) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nnc2c1[C@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2) `ZINC001142696197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696197 none CCn1nnc2c1[C@H](COC)CN(C(=O)[C@](C)([O-])[SiH3])C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 43, 12, 5, 1, 9, 1, 1, 1, 12, 30, 30, 30, 30, 30, 33, 33, 43, 43, 43, 12, 12, 1, 1, 1, 12, 12] 50 rigid atoms, others: [32, 33, 34, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 223 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696197 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696197 Building ZINC001142696242 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696242 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/586 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1) `ZINC001142696242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696242 none C[C@@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 123 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/587 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1) `ZINC001142696242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696242 none C[C@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 50, 50, 50, 50, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 24, 24, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696242 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 Building ZINC001142696242 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696242 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 586) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1) `ZINC001142696242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696242 none C[C@@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 123 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 587) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1) `ZINC001142696242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142696242 none C[C@]([O-])([SiH3])C(=O)N1CCCn2nnc(Cn3ccnc3)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 8, 8, 1, 5, 8, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 50, 50, 50, 50, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 24, 24, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696242 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696242 Building ZINC001142696377 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696377 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/588 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])C3)n1) `ZINC001142696377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142696377 none Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])C3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 17, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17, 29, 30, 31] 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, 32, 33]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/589 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])C3)n1) `ZINC001142696377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142696377 none Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])C3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 17, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17, 29, 30, 31] 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, 32, 33]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696377 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 Building ZINC001142696377 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696377 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 588) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])C3)n1) `ZINC001142696377.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142696377 none Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@@](C)([O-])[SiH3])C3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 17, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17, 29, 30, 31] 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, 32, 33]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 589) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])C3)n1) `ZINC001142696377.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142696377 none Cc1noc([C@]23COC[C@H]2CN(C(=O)[C@](C)([O-])[SiH3])C3)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 4, 1, 8, 1, 1, 1, 17, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 17, 17] 50 rigid atoms, others: [13, 15, 16, 17, 29, 30, 31] 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, 32, 33]) total number of confs: 79 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696377 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696377 Building ZINC001142696393 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696393 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/590 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@](C)([O-])[SiH3])C2)C1) `ZINC001142696393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696393 none CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@](C)([O-])[SiH3])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 1, 9, 1, 1, 1, 26, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 25, 26, 26, 1, 1, 1, 22, 26, 26, 26] 50 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/591 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@@](C)([O-])[SiH3])C2)C1) `ZINC001142696393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696393 none CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@@](C)([O-])[SiH3])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 22, 4, 1, 8, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 21, 23, 23, 23] 50 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696393 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 Building ZINC001142696393 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696393 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 590) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@](C)([O-])[SiH3])C2)C1) `ZINC001142696393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696393 none CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@](C)([O-])[SiH3])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 26, 4, 1, 9, 1, 1, 1, 26, 26, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 25, 26, 26, 1, 1, 1, 22, 26, 26, 26] 50 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 591) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@@](C)([O-])[SiH3])C2)C1) `ZINC001142696393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001142696393 none CN(C)C(=O)N[C@@H]1CCO[C@]2(CCN(C(=O)[C@@](C)([O-])[SiH3])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 22, 4, 1, 8, 1, 1, 1, 23, 23, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 21, 23, 23, 23] 50 rigid atoms, others: [37, 38, 39, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696393 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696393 Building ZINC001142696404 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696404 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/592 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1) `ZINC001142696404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696404 none Cn1cc(N2C[C@@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 21, 21, 21, 21, 21, 5, 1, 10, 1, 1, 1, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [32, 10, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/593 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1) `ZINC001142696404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696404 none Cn1cc(N2C[C@@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 21, 21, 21, 21, 21, 5, 1, 10, 1, 1, 1, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [32, 10, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696404 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 Building ZINC001142696404 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696404 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 592) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1) `ZINC001142696404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696404 none Cn1cc(N2C[C@@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 21, 21, 21, 21, 21, 5, 1, 10, 1, 1, 1, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [32, 10, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 593) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(N2C[C@@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1) `ZINC001142696404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142696404 none Cn1cc(N2C[C@@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]3C2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 5, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 1, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 21, 21, 21, 21, 21, 21, 5, 1, 10, 1, 1, 1, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [32, 10, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696404 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696404 Building ZINC001142696412 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696412 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/594 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/595 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/596 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/596' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/597 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/597' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696412 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 Building ZINC001142696412 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696412 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 594) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 595) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 596) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 597) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696412 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 Building ZINC001142696412 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696412 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 594) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 595) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 596) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 597) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696412 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 Building ZINC001142696412 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696412 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 594) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 595) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 596) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 50, 31, 31, 31, 31, 31, 31, 31, 31, 16, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 42, 42, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 597) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142696412.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001142696412 none CNC(=O)CN1CCCC12CCN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 50, 31, 31, 31, 31, 31, 31, 31, 31, 14, 1, 20, 1, 1, 1, 31, 31, 50, 50, 50, 50, 41, 41, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [36, 37, 38, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696412 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696412 Building ZINC001142696501 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696501 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/598 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142696501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142696501 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 50, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 2, 18, 1, 1, 1, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 33, 33] 50 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 125 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/599 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142696501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142696501 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 2, 18, 1, 1, 1, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 35, 35] 50 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 118 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696501 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 Building ZINC001142696501 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696501 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 598) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142696501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142696501 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 50, 33, 33, 33, 33, 33, 33, 33, 33, 33, 14, 2, 18, 1, 1, 1, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 33, 33] 50 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 125 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 599) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21) `ZINC001142696501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142696501 none CN(C)C(=O)[C@@H]1CCO[C@@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 50, 35, 35, 35, 35, 35, 35, 35, 35, 35, 14, 2, 18, 1, 1, 1, 35, 35, 35, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 35, 35] 50 rigid atoms, others: [37, 38, 39, 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, 40, 41]) total number of confs: 118 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696501 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696501 Building ZINC001142696513 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696513 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/600 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142696513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696513 none CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 24, 1, 24, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 1, 1, 1, 29, 29] 50 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/601 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142696513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696513 none CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 1, 22, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 1, 1, 1, 27, 27] 50 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 193 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696513 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 Building ZINC001142696513 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696513 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 600) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142696513.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696513 none CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 24, 1, 24, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 29, 29, 29, 1, 1, 1, 29, 29] 50 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 601) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142696513.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696513 none CN(C)C[C@@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 22, 1, 22, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 27, 1, 1, 1, 27, 27] 50 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 193 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696513 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696513 Building ZINC001142696515 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696515 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/602 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142696515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696515 none CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 1, 12, 1, 1, 1, 20, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20] 35 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/603 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142696515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696515 none CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 1, 12, 1, 1, 1, 19, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19] 32 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 117 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696515 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 Building ZINC001142696515 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696515 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 602) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142696515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696515 none CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 1, 12, 1, 1, 1, 20, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 20, 20, 20, 20, 1, 1, 1, 20, 20] 35 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 131 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 603) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142696515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696515 none CN(C)C[C@H]1Cn2ccnc2CN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 7, 5, 8, 1, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 1, 12, 1, 1, 1, 19, 32, 32, 32, 32, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 1, 1, 1, 19, 19] 32 rigid atoms, others: [34, 35, 36, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 117 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696515 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696515 Building ZINC001142696571 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696571 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/604 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2) `ZINC001142696571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142696571 none C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 32, 46, 46, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 32, 32, 46, 46, 46, 46, 46, 11, 11, 11, 11] 46 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/605 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2) `ZINC001142696571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142696571 none C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 36, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 36, 36, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696571 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 Building ZINC001142696571 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696571 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 604) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2) `ZINC001142696571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142696571 none C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 32, 46, 46, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11, 32, 32, 46, 46, 46, 46, 46, 11, 11, 11, 11] 46 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 605) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2) `ZINC001142696571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142696571 none C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(CC3CC3)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 12, 36, 50, 50, 12, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 36, 36, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696571 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696571 Building ZINC001142696578 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696578 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/606 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21) `ZINC001142696578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696578 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 15, 15, 15, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 15, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/607 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21) `ZINC001142696578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696578 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 15, 15, 15, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 15, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696578 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 Building ZINC001142696578 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696578 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 606) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21) `ZINC001142696578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696578 none C[C@@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 15, 15, 15, 50, 50, 50, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 15, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 607) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21) `ZINC001142696578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696578 none C[C@]([O-])([SiH3])C(=O)N1C[C@@H](NC(=O)C2CCC2)[C@H]2COC[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 15, 15, 15, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 15, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696578 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696578 Building ZINC001142696616 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696616 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/608 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/609 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/610 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/610' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/611 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/611' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696616 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 Building ZINC001142696616 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696616 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 608) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 609) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 610) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 611) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696616 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 Building ZINC001142696616 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696616 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 608) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 609) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 610) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 611) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696616 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 Building ZINC001142696616 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142696616 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 608) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 609) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 29, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 610) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 611) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1) `ZINC001142696616.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142696616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696616 none Cc1ccc(N2CCO[C@H]3CN(C(=O)[C@](C)([O-])[SiH3])C[C@H]32)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 31, 27, 4, 1, 12, 1, 1, 1, 31, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31, 31, 31, 1, 1, 1, 31, 31] 50 rigid atoms, others: [34, 35, 36, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696616 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696616 Building ZINC001142696620 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696620 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/612 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O) `ZINC001142696620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696620 none CCN1C[C@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 45, 45, 45, 43, 31, 1, 36, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 1, 1, 1, 45, 45, 45, 45] 50 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/613 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H]2CCN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O) `ZINC001142696620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696620 none CCN1C[C@H]2CCN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 46, 46, 44, 30, 1, 35, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 1, 1, 1, 46, 46, 46, 46] 50 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696620 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 Building ZINC001142696620 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696620 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 612) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O) `ZINC001142696620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696620 none CCN1C[C@H]2CCN(C(=O)[C@@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 45, 45, 45, 45, 43, 31, 1, 36, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 45, 45, 45, 45, 45, 45, 1, 1, 1, 45, 45, 45, 45] 50 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 613) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H]2CCN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O) `ZINC001142696620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142696620 none CCN1C[C@H]2CCN(C(=O)[C@](C)([O-])[SiH3])CC[C@H]2S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 46, 46, 46, 46, 44, 30, 1, 35, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 46, 1, 1, 1, 46, 46, 46, 46] 50 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696620 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696620 Building ZINC001142696631 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696631 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/614 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1) `ZINC001142696631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142696631 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 10, 22, 28, 28, 28, 28, 37, 37, 37, 37, 37, 28, 28, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 37 rigid atoms, others: [0, 1, 2, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/615 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1) `ZINC001142696631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142696631 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 19, 26, 26, 25, 26, 34, 34, 34, 34, 34, 26, 26, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 34 rigid atoms, others: [0, 1, 2, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696631 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 Building ZINC001142696631 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696631 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 614) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1) `ZINC001142696631.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142696631 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 10, 22, 28, 28, 28, 28, 37, 37, 37, 37, 37, 28, 28, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 37 rigid atoms, others: [0, 1, 2, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 615) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1) `ZINC001142696631.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142696631 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)C(F)(F)F)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 15, 15, 15, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 19, 26, 26, 25, 26, 34, 34, 34, 34, 34, 26, 26, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 34 rigid atoms, others: [0, 1, 2, 17, 18, 19] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 78 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696631 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696631 Building ZINC001142696718 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696718 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/616 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1) `ZINC001142696718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696718 none C[C@@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 10, 5, 5, 12, 5, 5, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 7, 8, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 21, 22, 23] set([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]) total number of confs: 138 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/617 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1) `ZINC001142696718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696718 none C[C@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 10, 5, 5, 12, 5, 5, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 30, 50, 50, 50, 50, 49, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 21, 22, 23] set([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]) total number of confs: 146 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696718 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 Building ZINC001142696718 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142696718 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 616) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1) `ZINC001142696718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696718 none C[C@@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 10, 5, 5, 12, 5, 5, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 7, 8, 8, 8, 8, 8, 29, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 21, 22, 23] set([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]) total number of confs: 138 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 617) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1) `ZINC001142696718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142696718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142696718 none C[C@]([O-])([SiH3])C(=O)N1CCn2c(CN3CCOCC3)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 10, 5, 5, 12, 5, 5, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 7, 7, 7, 7, 7, 7, 30, 50, 50, 50, 50, 49, 7, 7, 7, 7, 1, 1, 1, 7, 7, 7, 7, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 21, 22, 23] set([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]) total number of confs: 146 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142696718 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142696718 Building ZINC001142697566 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697566 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/618 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1) `ZINC001142697566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697566 none C[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 12, 32, 40, 40, 40, 50, 50, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 40, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/619 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1) `ZINC001142697566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697566 none C[C@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 11, 31, 40, 40, 40, 50, 50, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 40, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697566 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 Building ZINC001142697566 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697566 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 618) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1) `ZINC001142697566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697566 none C[C@@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 12, 32, 40, 40, 40, 50, 50, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 32, 32, 40, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 619) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1) `ZINC001142697566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697566 none C[C@]([O-])([SiH3])C(=O)N1CCC(OCC(=O)NC2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 11, 31, 40, 40, 40, 50, 50, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 40, 50, 50, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 180 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697566 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697566 Building ZINC001142697628 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697628 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/620 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001142697628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697628 none C[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 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: [9, 8, 10, 11, 6, 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: [1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 13, 19, 24, 50, 50, 50, 8, 8, 1, 1, 1, 8, 8, 8, 8, 13, 13, 19, 19, 24, 24, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/621 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001142697628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697628 none C[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 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: [9, 8, 10, 11, 6, 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: [1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 13, 21, 26, 50, 50, 50, 8, 8, 1, 1, 1, 8, 8, 8, 8, 13, 13, 21, 21, 26, 26, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 242 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697628 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 Building ZINC001142697628 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697628 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 620) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001142697628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697628 none C[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 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: [9, 8, 10, 11, 6, 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: [1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 13, 19, 24, 50, 50, 50, 8, 8, 1, 1, 1, 8, 8, 8, 8, 13, 13, 19, 19, 24, 24, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 233 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 621) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001142697628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697628 none C[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 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: [9, 8, 10, 11, 6, 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: [1, 1, 1, 1, 3, 5, 8, 8, 8, 8, 13, 21, 26, 50, 50, 50, 8, 8, 1, 1, 1, 8, 8, 8, 8, 13, 13, 21, 21, 26, 26, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 242 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697628 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697628 Building ZINC001142697641 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697641 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/622 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697641 none CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 37, 8, 37, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/623 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697641 none CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 35, 10, 35, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697641 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 Building ZINC001142697641 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697641 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 622) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697641.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697641 none CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 37, 8, 37, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 623) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697641.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697641 none CCOC(=O)[C@@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 35, 10, 35, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 124 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697641 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697641 Building ZINC001142697642 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697642 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/624 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697642 none CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 35, 10, 35, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 128 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/625 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697642 none CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 38, 8, 38, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697642 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 Building ZINC001142697642 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697642 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 624) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697642 none CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 35, 10, 35, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 50, 50, 50, 50, 50, 10, 10, 10, 10, 10, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 128 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 625) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697642 none CCOC(=O)[C@H]1c2[nH]cnc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 6, 1, 8, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 38, 8, 38, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697642 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697642 Building ZINC001142697647 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697647 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/626 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1) `ZINC001142697647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697647 none C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 30, 33, 44, 44, 44, 44, 44, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/627 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1) `ZINC001142697647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697647 none C[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 30, 32, 47, 47, 47, 47, 47, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 47, 47, 47, 47, 47, 47, 47, 47] 47 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697647 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 Building ZINC001142697647 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697647 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 626) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1) `ZINC001142697647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697647 none C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 30, 33, 44, 44, 44, 44, 44, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 44, 44, 44, 44, 44, 44, 44, 44] 44 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 627) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1) `ZINC001142697647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697647 none C[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 30, 32, 47, 47, 47, 47, 47, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 47, 47, 47, 47, 47, 47, 47, 47] 47 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697647 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697647 Building ZINC001142697648 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697648 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/628 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1) `ZINC001142697648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697648 none C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 31, 31, 50, 50, 50, 50, 50, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/629 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1) `ZINC001142697648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697648 none C[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 30, 31, 48, 48, 48, 48, 48, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 48] 48 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697648 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 Building ZINC001142697648 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697648 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 628) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1) `ZINC001142697648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697648 none C[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13, 31, 31, 50, 50, 50, 50, 50, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 629) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1) `ZINC001142697648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697648 none C[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 30, 31, 48, 48, 48, 48, 48, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 48, 48, 48, 48, 48, 48, 48, 48] 48 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 110 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697648 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697648 Building ZINC001142697711 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697711 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/630 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001142697711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142697711 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 13, 23, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 24, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/631 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001142697711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142697711 none C[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 13, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697711 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 Building ZINC001142697711 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697711 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 630) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001142697711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142697711 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 13, 23, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 24, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 631) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001142697711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142697711 none C[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 13, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697711 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697711 Building ZINC001142697732 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697732 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/632 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1) `ZINC001142697732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697732 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 12, 24, 24, 24, 24, 45, 45, 50, 50, 47, 50, 50, 24, 24, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/633 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1) `ZINC001142697732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697732 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 12, 23, 23, 21, 23, 44, 44, 50, 50, 44, 50, 50, 23, 23, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697732 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 Building ZINC001142697732 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697732 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 632) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1) `ZINC001142697732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697732 none C[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 8, 12, 24, 24, 24, 24, 45, 45, 50, 50, 47, 50, 50, 24, 24, 1, 1, 1, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 135 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 633) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1) `ZINC001142697732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697732 none C[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2ccncc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 7, 12, 23, 23, 21, 23, 44, 44, 50, 50, 44, 50, 50, 23, 23, 1, 1, 1, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 153 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697732 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697732 Building ZINC001142697791 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697791 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/634 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@](C)([O-])[SiH3])CC2)ncn1) `ZINC001142697791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697791 none COc1cc(N2CCN(C(=O)[C@](C)([O-])[SiH3])CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 15, 15, 15, 15, 11, 2, 14, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 15, 15, 15, 15, 50] 50 rigid atoms, others: [11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/635 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@@](C)([O-])[SiH3])CC2)ncn1) `ZINC001142697791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697791 none COc1cc(N2CCN(C(=O)[C@@](C)([O-])[SiH3])CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 14, 14, 14, 14, 10, 1, 12, 1, 1, 1, 14, 14, 48, 48, 48, 50, 50, 50, 48, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 48] 50 rigid atoms, others: [9, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697791 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 Building ZINC001142697791 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697791 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 634) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@](C)([O-])[SiH3])CC2)ncn1) `ZINC001142697791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697791 none COc1cc(N2CCN(C(=O)[C@](C)([O-])[SiH3])CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 15, 15, 15, 15, 11, 2, 14, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 1, 1, 1, 15, 15, 15, 15, 50] 50 rigid atoms, others: [11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 635) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@@](C)([O-])[SiH3])CC2)ncn1) `ZINC001142697791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 4 11 3 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697791 none COc1cc(N2CCN(C(=O)[C@@](C)([O-])[SiH3])CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 14, 14, 14, 14, 10, 1, 12, 1, 1, 1, 14, 14, 48, 48, 48, 50, 50, 50, 48, 14, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 48] 50 rigid atoms, others: [9, 11, 12, 13, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697791 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697791 Building ZINC001142697838 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697838 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/636 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697838 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 23, 35, 35, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 8, 8, 8, 8, 23, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/637 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697838 none C[C@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 18, 32, 32, 32, 50, 50, 50, 50, 50, 7, 1, 1, 1, 7, 7, 7, 7, 18, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697838 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 Building ZINC001142697838 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697838 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 636) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697838 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 23, 35, 35, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 8, 8, 8, 8, 23, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 637) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697838 none C[C@]([O-])([SiH3])C(=O)N1CC[C@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 18, 32, 32, 32, 50, 50, 50, 50, 50, 7, 1, 1, 1, 7, 7, 7, 7, 18, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697838 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697838 Building ZINC001142697845 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697845 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/638 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697845 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 22, 35, 35, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 8, 8, 8, 8, 22, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/639 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697845 none C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 24, 34, 34, 34, 50, 50, 50, 50, 50, 8, 1, 1, 1, 8, 8, 8, 8, 24, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 146 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697845 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 Building ZINC001142697845 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697845 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 638) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697845.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697845 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 22, 35, 35, 35, 50, 50, 50, 50, 50, 8, 1, 1, 1, 8, 8, 8, 8, 22, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 639) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1) `ZINC001142697845.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142697845 none C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NS(=O)(=O)c2ccccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 24, 34, 34, 34, 50, 50, 50, 50, 50, 8, 1, 1, 1, 8, 8, 8, 8, 24, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 146 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697845 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697845 Building ZINC001142697884 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697884 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/640 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697884 none CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 7, 41, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 114 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/641 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697884 none CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 9, 43, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 115 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697884 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 Building ZINC001142697884 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697884 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 640) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697884 none CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 7, 41, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 114 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 641) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697884 none CCOC(=O)[C@@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 9, 43, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 115 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697884 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697884 Building ZINC001142697885 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697885 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/642 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697885 none CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 8, 42, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/643 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697885 none CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 7, 42, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 114 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697885 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 Building ZINC001142697885 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697885 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 642) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142697885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697885 none CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 8, 42, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 1, 7, 1, 1, 1, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 643) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142697885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142697885 none CCOC(=O)[C@H]1c2n[nH]cc2CCN1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 1, 8, 8, 6, 1, 1, 5, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 42, 7, 42, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7, 1, 1, 1] 50 rigid atoms, others: [32, 33, 16, 18, 19, 20, 31] 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]) total number of confs: 114 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697885 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697885 Building ZINC001142697894 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697894 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/644 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CN1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142697894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697894 none CC(C)NC(=O)CN1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 50, 12, 12, 12, 12, 7, 1, 4, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/645 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CN1CCN(C(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142697894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697894 none CC(C)NC(=O)CN1CCN(C(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 50, 12, 12, 12, 12, 8, 1, 4, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697894 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 Building ZINC001142697894 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697894 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 644) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CN1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142697894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697894 none CC(C)NC(=O)CN1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 50, 12, 12, 12, 12, 7, 1, 4, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 29, 29, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 164 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 645) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)CN1CCN(C(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142697894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142697894 none CC(C)NC(=O)CN1CCN(C(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 50, 12, 12, 12, 12, 8, 1, 4, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697894 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697894 Building ZINC001142697957 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697957 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/646 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001142697957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142697957 none C[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 12, 15, 15, 15, 15, 38, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 15, 15, 15, 15, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/647 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001142697957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142697957 none C[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 13, 16, 16, 16, 16, 39, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 16, 16, 16, 16, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697957 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 Building ZINC001142697957 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697957 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 646) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001142697957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142697957 none C[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 12, 15, 15, 15, 15, 38, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 15, 15, 15, 15, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 647) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001142697957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001142697957 none C[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 13, 16, 16, 16, 16, 39, 50, 50, 50, 50, 50, 50, 16, 16, 1, 1, 1, 16, 16, 16, 16, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697957 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697957 Building ZINC001142697986 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697986 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/648 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@@](C)([O-])[SiH3])CCC2) `ZINC001142697986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697986 none CC(=O)NCc1ncn2c1CN(C(=O)[C@@](C)([O-])[SiH3])CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 14, 14, 14, 14, 14, 14, 14, 6, 1, 14, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 47, 47, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 14, 15, 16, 29, 30, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 181 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/649 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@](C)([O-])[SiH3])CCC2) `ZINC001142697986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697986 none CC(=O)NCc1ncn2c1CN(C(=O)[C@](C)([O-])[SiH3])CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 12, 12, 12, 12, 12, 12, 12, 5, 1, 12, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 42, 42, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 14, 15, 16, 29, 30, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697986 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 Building ZINC001142697986 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142697986 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 648) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@@](C)([O-])[SiH3])CCC2) `ZINC001142697986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142697986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697986 none CC(=O)NCc1ncn2c1CN(C(=O)[C@@](C)([O-])[SiH3])CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 14, 14, 14, 14, 14, 14, 14, 6, 1, 14, 1, 1, 1, 14, 14, 14, 50, 50, 50, 50, 47, 47, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [12, 14, 15, 16, 29, 30, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 181 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 649) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCc1ncn2c1CN(C(=O)[C@](C)([O-])[SiH3])CCC2) `ZINC001142697986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142697986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142697986 none CC(=O)NCc1ncn2c1CN(C(=O)[C@](C)([O-])[SiH3])CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 8, 1, 8, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 12, 12, 12, 12, 12, 12, 12, 5, 1, 12, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 42, 42, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [12, 14, 15, 16, 29, 30, 31] 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, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142697986 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142697986 Building ZINC001142698052 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698052 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/650 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2) `ZINC001142698052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142698052 none C[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/651 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2) `ZINC001142698052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142698052 none C[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 9, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698052 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 Building ZINC001142698052 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698052 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 650) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2) `ZINC001142698052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142698052 none C[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 651) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2) `ZINC001142698052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142698052 none C[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CC(=O)NC(=O)C2 NO_LONG_NAME dock atom types: ['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.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 2, 9, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698052 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698052 Building ZINC001142698070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/652 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001142698070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142698070 none C[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 12, 23, 29, 29, 29, 29, 43, 43, 29, 29, 43, 43, 29, 29, 1, 1, 1, 29, 29, 29, 29, 43, 86, 43, 29, 29, 29, 29] 86 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/653 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001142698070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142698070 none C[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 12, 23, 30, 30, 30, 30, 42, 42, 30, 30, 42, 42, 30, 30, 1, 1, 1, 30, 30, 30, 30, 42, 84, 42, 30, 30, 30, 30] 84 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 Building ZINC001142698070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 652) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001142698070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142698070 none C[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 12, 23, 29, 29, 29, 29, 43, 43, 29, 29, 43, 43, 29, 29, 1, 1, 1, 29, 29, 29, 29, 43, 86, 43, 29, 29, 29, 29] 86 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 653) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001142698070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142698070 none C[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 12, 23, 30, 30, 30, 30, 42, 42, 30, 30, 42, 42, 30, 30, 1, 1, 1, 30, 30, 30, 30, 42, 84, 42, 30, 30, 30, 30] 84 rigid atoms, others: [0, 1, 2, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 185 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698070 Building ZINC001142698215 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698215 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/654 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn2c(n1)CN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142698215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698215 none COC(=O)c1cn2c(n1)CN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 14, 50, 14, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 14, 14, 50, 50, 50, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/655 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn2c(n1)CN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142698215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698215 none COC(=O)c1cn2c(n1)CN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 14, 50, 14, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 14, 14, 50, 50, 50, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698215 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 Building ZINC001142698215 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698215 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 654) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn2c(n1)CN(C(=O)[C@](C)([O-])[SiH3])CC2) `ZINC001142698215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698215 none COC(=O)c1cn2c(n1)CN(C(=O)[C@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 14, 50, 14, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 14, 14, 50, 50, 50, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 655) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn2c(n1)CN(C(=O)[C@@](C)([O-])[SiH3])CC2) `ZINC001142698215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698215 none COC(=O)c1cn2c(n1)CN(C(=O)[C@@](C)([O-])[SiH3])CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 14, 50, 14, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 14, 14, 50, 50, 50, 14, 14, 14, 1, 1, 1, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30]) total number of confs: 123 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698215 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698215 Building ZINC001142698229 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698229 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/656 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O) `ZINC001142698229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698229 none CCOC(=O)[C@@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 16, 4, 16, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 23 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/657 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O) `ZINC001142698229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698229 none CCOC(=O)[C@@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 17, 4, 17, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 28, 28, 28, 28, 28, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 28 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698229 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 Building ZINC001142698229 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698229 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 656) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O) `ZINC001142698229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698229 none CCOC(=O)[C@@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 20, 16, 4, 16, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 23, 23, 23, 23, 23, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 23 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 67 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 657) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O) `ZINC001142698229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698229 none CCOC(=O)[C@@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 17, 4, 17, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 28, 28, 28, 28, 28, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 28 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698229 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698229 Building ZINC001142698230 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698230 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/658 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O) `ZINC001142698230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698230 none CCOC(=O)[C@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 43, 13, 43, 13, 13, 13, 13, 12, 1, 12, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/659 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O) `ZINC001142698230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698230 none CCOC(=O)[C@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 43, 12, 43, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698230 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 Building ZINC001142698230 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698230 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 658) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O) `ZINC001142698230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698230 none CCOC(=O)[C@H]1CCN(C(=O)[C@@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 43, 13, 43, 13, 13, 13, 13, 12, 1, 12, 1, 1, 1, 13, 13, 13, 13, 50, 50, 50, 50, 50, 13, 13, 13, 13, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 659) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O) `ZINC001142698230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142698230 none CCOC(=O)[C@H]1CCN(C(=O)[C@](C)([O-])[SiH3])CCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 43, 12, 43, 12, 12, 12, 12, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698230 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698230 Building ZINC001142698287 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698287 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/660 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698287 none COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 14, 5, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 2, 1, 2, 1, 1, 1, 9, 9, 9, 4, 4, 10, 10, 10, 1, 1, 1] 22 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/661 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698287 none COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 14, 5, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 2, 1, 2, 1, 1, 1, 9, 9, 9, 4, 4, 12, 12, 12, 1, 1, 1] 25 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698287 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 Building ZINC001142698287 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698287 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 660) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698287 none COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 14, 5, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 2, 1, 2, 1, 1, 1, 9, 9, 9, 4, 4, 10, 10, 10, 1, 1, 1] 22 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 661) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698287 none COC(=O)[C@H]1SC[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 14, 5, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 4, 9, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 2, 1, 2, 1, 1, 1, 9, 9, 9, 4, 4, 12, 12, 12, 1, 1, 1] 25 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698287 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698287 Building ZINC001142698292 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698292 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/662 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698292 none COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 14, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 5, 1, 5, 1, 1, 1, 14, 14, 14, 5, 5, 13, 13, 13, 1, 1, 1] 32 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/663 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698292 none COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 5, 1, 5, 1, 1, 1, 12, 12, 12, 5, 5, 13, 13, 13, 1, 1, 1] 27 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698292 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 Building ZINC001142698292 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698292 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 662) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698292 none COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 14, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 5, 1, 5, 1, 1, 1, 14, 14, 14, 5, 5, 13, 13, 13, 1, 1, 1] 32 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 663) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698292 none COC(=O)[C@@H]1CS[C@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 5, 1, 5, 1, 1, 1, 12, 12, 12, 5, 5, 13, 13, 13, 1, 1, 1] 27 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698292 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698292 Building ZINC001142698294 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698294 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/664 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698294 none COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 14, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 5, 1, 5, 1, 1, 1, 14, 14, 14, 5, 5, 12, 12, 12, 1, 1, 1] 31 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/665 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698294 none COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 5, 1, 5, 1, 1, 1, 12, 12, 12, 5, 5, 12, 12, 12, 1, 1, 1] 27 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698294 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 Building ZINC001142698294 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698294 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 664) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698294 none COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 5, 14, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 5, 1, 5, 1, 1, 1, 14, 14, 14, 5, 5, 12, 12, 12, 1, 1, 1] 31 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 665) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698294 none COC(=O)[C@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 5, 1, 5, 1, 1, 1, 12, 12, 12, 5, 5, 12, 12, 12, 1, 1, 1] 27 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698294 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698294 Building ZINC001142698295 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698295 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/666 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698295 none COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 4, 12, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 2, 1, 2, 1, 1, 1, 12, 12, 12, 4, 4, 8, 8, 8, 1, 1, 1] 23 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/667 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698295 none COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 2, 1, 2, 1, 1, 1, 7, 7, 7, 3, 3, 7, 7, 7, 1, 1, 1] 15 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 31 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698295 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 Building ZINC001142698295 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698295 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 666) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3]) `ZINC001142698295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698295 none COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 4, 12, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 2, 1, 2, 1, 1, 1, 12, 12, 12, 4, 4, 8, 8, 8, 1, 1, 1] 23 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 667) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3]) `ZINC001142698295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142698295 none COC(=O)[C@@H]1CS[C@@H](C(=O)OC)N1C(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 14, 5, 7, 1, 11, 12, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 2, 1, 2, 1, 1, 1, 7, 7, 7, 3, 3, 7, 7, 7, 1, 1, 1] 15 rigid atoms, others: [15, 17, 18, 19, 28, 29, 30] 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]) total number of confs: 31 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698295 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698295 Building ZINC001142698335 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698335 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/668 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142698335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698335 none CCNC(=O)CO[C@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 24, 32, 9, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 50, 50, 50, 50, 50, 32, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 50 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/669 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142698335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698335 none CCNC(=O)CO[C@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 24, 31, 9, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 5, 50, 50, 50, 50, 50, 31, 24, 24, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5] 50 rigid atoms, others: [33, 34, 35, 15, 16, 17] 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, 36, 37]) total number of confs: 222 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698335 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 Building ZINC001142698335 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698335 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 668) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142698335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698335 none CCNC(=O)CO[C@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 24, 32, 9, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 50, 50, 50, 50, 50, 32, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 50 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 220 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 669) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142698335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698335 none CCNC(=O)CO[C@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 24, 31, 9, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 5, 50, 50, 50, 50, 50, 31, 24, 24, 5, 5, 5, 5, 5, 5, 1, 1, 1, 5, 5] 50 rigid atoms, others: [33, 34, 35, 15, 16, 17] 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, 36, 37]) total number of confs: 222 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698335 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698335 Building ZINC001142698338 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698338 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/670 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142698338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698338 none CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 24, 31, 10, 4, 4, 4, 4, 4, 4, 4, 1, 3, 1, 1, 1, 4, 50, 50, 50, 50, 50, 31, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 50 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 220 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/671 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142698338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698338 none CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 26, 33, 11, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 50, 50, 50, 50, 50, 33, 26, 26, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 50 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698338 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 Building ZINC001142698338 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698338 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 670) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142698338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698338 none CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 24, 31, 10, 4, 4, 4, 4, 4, 4, 4, 1, 3, 1, 1, 1, 4, 50, 50, 50, 50, 50, 31, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 50 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 220 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 671) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142698338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142698338 none CCNC(=O)CO[C@@H]1CCCN(C(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 26, 33, 11, 4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 4, 50, 50, 50, 50, 50, 33, 26, 26, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4] 50 rigid atoms, others: [33, 34, 35, 13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698338 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698338 Building ZINC001142698949 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698949 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/672 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1) `ZINC001142698949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142698949 none C[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 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: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 50, 50, 50, 50, 34, 50, 50, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/673 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1) `ZINC001142698949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142698949 none C[C@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 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: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 50, 50, 50, 50, 36, 50, 50, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698949 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 Building ZINC001142698949 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142698949 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 672) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1) `ZINC001142698949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142698949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142698949 none C[C@@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 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: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 50, 50, 50, 50, 34, 50, 50, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 673) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1) `ZINC001142698949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142698949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142698949 none C[C@]([O-])([SiH3])C(=O)N1CCC(N2CCCCS2(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 14, 11, 11, 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: [9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 50, 50, 50, 50, 36, 50, 50, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142698949 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142698949 Building ZINC001142699072 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699072 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/674 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001142699072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142699072 none C[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 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: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 39, 39, 39, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 39, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/675 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001142699072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142699072 none C[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 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: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 41, 41, 41, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 41, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699072 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 Building ZINC001142699072 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699072 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 674) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001142699072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142699072 none C[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 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: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 39, 39, 39, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 11, 11, 11, 11, 11, 39, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 675) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001142699072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142699072 none C[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 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: [9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 7, 12, 12, 12, 12, 41, 41, 41, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 12, 12, 12, 12, 12, 41, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 120 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699072 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699072 Building ZINC001142699090 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699090 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/676 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1) `ZINC001142699090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142699090 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 16, 16, 22, 22, 22, 22, 22, 50, 50, 50, 50, 48, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/677 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1) `ZINC001142699090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142699090 none C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 15, 15, 20, 20, 20, 20, 20, 50, 50, 50, 50, 49, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699090 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 Building ZINC001142699090 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699090 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 676) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1) `ZINC001142699090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142699090 none C[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 16, 16, 22, 22, 22, 22, 22, 50, 50, 50, 50, 48, 22, 22, 22, 22, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 677) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1) `ZINC001142699090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142699090 none C[C@]([O-])([SiH3])C(=O)N1CC[C@@H](N2CCOCC2)[C@@H](F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 12, 5, 5, 5, 7, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 15, 15, 20, 20, 20, 20, 20, 50, 50, 50, 50, 49, 20, 20, 20, 20, 1, 1, 1, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699090 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699090 Building ZINC001142699148 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699148 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/678 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142699148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699148 none CCS(=O)(=O)NC1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 23, 32, 32, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 23, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 218 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/679 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1CCN(C(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142699148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699148 none CCS(=O)(=O)NC1CCN(C(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 22, 31, 31, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 22, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699148 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 Building ZINC001142699148 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699148 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 678) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142699148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699148 none CCS(=O)(=O)NC1CCN(C(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 23, 32, 32, 11, 11, 11, 11, 4, 1, 4, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 23, 11, 11, 11, 11, 11, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 218 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 679) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1CCN(C(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142699148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 4 12 3 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699148 none CCS(=O)(=O)NC1CCN(C(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 22, 31, 31, 9, 9, 9, 9, 3, 1, 3, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 22, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699148 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699148 Building ZINC001142699244 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699244 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/680 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O) `ZINC001142699244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142699244 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/681 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O) `ZINC001142699244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142699244 none C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699244 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 Building ZINC001142699244 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699244 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 680) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O) `ZINC001142699244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142699244 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 681) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O) `ZINC001142699244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC001142699244 none C[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)S(=O)(=O)NC2=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 7, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699244 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699244 Building ZINC001142699276 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699276 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/682 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001142699276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142699276 none C[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 9, 17, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/683 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001142699276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142699276 none C[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 9, 17, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699276 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 Building ZINC001142699276 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699276 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 682) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001142699276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142699276 none C[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 9, 17, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 683) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001142699276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142699276 none C[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 50, 50, 50, 17, 17, 17, 17, 1, 1, 1, 9, 17, 50, 50, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699276 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699276 Building ZINC001142699303 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699303 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/684 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@](C)([O-])[SiH3])c1) `ZINC001142699303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142699303 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@](C)([O-])[SiH3])c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 5, 12, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 19, 30, 30, 19, 19, 19, 19, 19, 10, 10, 1, 10, 1, 1, 1, 19, 50, 50, 50, 50, 19, 19, 38, 10, 1, 1, 1, 19] 100 rigid atoms, others: [12, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/685 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@](C)([O-])[SiH3])c1) `ZINC001142699303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142699303 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@](C)([O-])[SiH3])c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 5, 12, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 20, 31, 31, 20, 16, 20, 20, 20, 8, 8, 1, 8, 1, 1, 1, 20, 50, 50, 50, 50, 20, 20, 40, 8, 1, 1, 1, 20] 100 rigid atoms, others: [12, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699303 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 Building ZINC001142699303 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699303 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 684) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@](C)([O-])[SiH3])c1) `ZINC001142699303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142699303 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@](C)([O-])[SiH3])c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 5, 12, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 30, 19, 30, 30, 19, 19, 19, 19, 19, 10, 10, 1, 10, 1, 1, 1, 19, 50, 50, 50, 50, 19, 19, 38, 10, 1, 1, 1, 19] 100 rigid atoms, others: [12, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 685) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@](C)([O-])[SiH3])c1) `ZINC001142699303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142699303 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@](C)([O-])[SiH3])c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 5, 12, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 20, 31, 31, 20, 16, 20, 20, 20, 8, 8, 1, 8, 1, 1, 1, 20, 50, 50, 50, 50, 20, 20, 40, 8, 1, 1, 1, 20] 100 rigid atoms, others: [12, 14, 15, 16, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699303 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699303 Building ZINC001142699507 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699507 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/686 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142699507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699507 none CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 32, 40, 18, 18, 18, 18, 18, 18, 8, 18, 5, 1, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 18, 18, 18, 18, 5, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/687 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142699507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699507 none CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 31, 41, 17, 17, 17, 17, 17, 17, 7, 17, 5, 1, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 17, 17, 5, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699507 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 Building ZINC001142699507 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699507 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 686) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142699507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699507 none CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 32, 40, 18, 18, 18, 18, 18, 18, 8, 18, 5, 1, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 18, 18, 18, 18, 5, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 687) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142699507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 4 18 3 22 to be deleted 23 to be deleted 24 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699507 none CC(C)(C)OC(=O)N[C@H]1COC[C@H]1NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 41, 31, 41, 17, 17, 17, 17, 17, 17, 7, 17, 5, 1, 5, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 17, 17, 17, 17, 5, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 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]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699507 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699507 Building ZINC001142699548 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699548 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/688 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1) `ZINC001142699548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142699548 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 11, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 4, 19, 36, 36, 36, 50, 50, 50, 5, 5, 1, 1, 1, 3, 5, 5, 19, 19, 36, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/689 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1) `ZINC001142699548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142699548 none C[C@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 11, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 12, 33, 33, 33, 48, 46, 47, 5, 5, 1, 1, 1, 3, 5, 5, 12, 12, 33, 50, 50, 48, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699548 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 Building ZINC001142699548 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699548 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 688) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1) `ZINC001142699548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142699548 none C[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 11, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 4, 19, 36, 36, 36, 50, 50, 50, 5, 5, 1, 1, 1, 3, 5, 5, 19, 19, 36, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 689) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1) `ZINC001142699548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001142699548 none C[C@]([O-])([SiH3])C(=O)Nc1ccc(CC(=O)NS(C)(=O)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 1, 11, 8, 14, 5, 11, 11, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 3, 12, 33, 33, 33, 48, 46, 47, 5, 5, 1, 1, 1, 3, 5, 5, 12, 12, 33, 50, 50, 48, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699548 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699548 Building ZINC001142699732 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699732 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/690 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1) `ZINC001142699732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142699732 none C[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 20, 33, 33, 33, 33, 50, 50, 50, 33, 33, 1, 1, 1, 5, 20, 20, 33, 33, 50, 50, 50, 33] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/691 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1) `ZINC001142699732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142699732 none C[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 20, 33, 33, 33, 33, 50, 50, 50, 33, 33, 1, 1, 1, 5, 20, 20, 33, 33, 50, 50, 50, 33] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699732 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 Building ZINC001142699732 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699732 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 690) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1) `ZINC001142699732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142699732 none C[C@@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 20, 33, 33, 33, 33, 50, 50, 50, 33, 33, 1, 1, 1, 5, 20, 20, 33, 33, 50, 50, 50, 33] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 691) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1) `ZINC001142699732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142699732 none C[C@]([O-])([SiH3])C(=O)NCc1ccc(S(C)(=O)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 20, 33, 33, 33, 33, 50, 50, 50, 33, 33, 1, 1, 1, 5, 20, 20, 33, 33, 50, 50, 50, 33] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699732 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699732 Building ZINC001142699735 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699735 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/692 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142699735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699735 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 15, 31, 15, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45, 4, 1, 1, 1, 15, 15] 150 rigid atoms, others: [34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/693 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142699735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699735 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 14, 28, 14, 14, 14, 14, 14, 6, 14, 4, 1, 4, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42, 4, 1, 1, 1, 14, 14] 150 rigid atoms, others: [34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699735 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 Building ZINC001142699735 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699735 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 692) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C1) `ZINC001142699735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699735 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 31, 15, 31, 15, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 45, 4, 1, 1, 1, 15, 15] 150 rigid atoms, others: [34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 693) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@](C)([O-])[SiH3])C1) `ZINC001142699735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001142699735 none CC(C)(C)OC(=O)N1C[C@@H](O)[C@H](NC(=O)[C@](C)([O-])[SiH3])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 8, 1, 11, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 28, 14, 28, 14, 14, 14, 14, 14, 6, 14, 4, 1, 4, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 42, 4, 1, 1, 1, 14, 14] 150 rigid atoms, others: [34, 35, 36, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699735 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699735 Building ZINC001142699941 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699941 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/694 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@@](C)([O-])[SiH3])c(=O)n(CC)c1=O) `ZINC001142699941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699941 none CCn1c(N)c(NC(=O)[C@@](C)([O-])[SiH3])c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 9, 9, 1, 9, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 9, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/695 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@](C)([O-])[SiH3])c(=O)n(CC)c1=O) `ZINC001142699941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699941 none CCn1c(N)c(NC(=O)[C@](C)([O-])[SiH3])c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 9, 9, 1, 9, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 9, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699941 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 Building ZINC001142699941 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142699941 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 694) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@@](C)([O-])[SiH3])c(=O)n(CC)c1=O) `ZINC001142699941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142699941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699941 none CCn1c(N)c(NC(=O)[C@@](C)([O-])[SiH3])c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 9, 9, 1, 9, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 9, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 695) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@](C)([O-])[SiH3])c(=O)n(CC)c1=O) `ZINC001142699941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142699941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142699941 none CCn1c(N)c(NC(=O)[C@](C)([O-])[SiH3])c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 9, 9, 1, 9, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 9, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142699941 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142699941 Building ZINC001142702656 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702656 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/696 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001142702656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702656 none C[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 12, 17, 17, 17, 28, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 3, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/697 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001142702656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702656 none C[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 12, 17, 17, 17, 27, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 3, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702656 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 Building ZINC001142702656 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702656 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 696) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001142702656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702656 none C[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 12, 17, 17, 17, 28, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 3, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 697) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001142702656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702656 none C[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 12, 17, 17, 17, 27, 50, 50, 50, 50, 50, 17, 17, 1, 1, 1, 3, 12, 12, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702656 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702656 Building ZINC001142702724 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702724 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/698 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C(=O)N1CCOCC1) `ZINC001142702724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702724 none CC(C)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 5, 15, 5, 1, 5, 1, 1, 1, 15, 35, 36, 44, 44, 44, 44, 44, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [6, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/699 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@](C)([O-])[SiH3])C(=O)N1CCOCC1) `ZINC001142702724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702724 none CC(C)[C@H](NC(=O)[C@](C)([O-])[SiH3])C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 14, 30, 5, 14, 5, 1, 5, 1, 1, 1, 14, 32, 32, 43, 43, 43, 43, 43, 31, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [6, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 206 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702724 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 Building ZINC001142702724 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702724 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 698) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C(=O)N1CCOCC1) `ZINC001142702724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702724 none CC(C)[C@H](NC(=O)[C@@](C)([O-])[SiH3])C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 15, 29, 5, 15, 5, 1, 5, 1, 1, 1, 15, 35, 36, 44, 44, 44, 44, 44, 29, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [6, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 699) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC(=O)[C@](C)([O-])[SiH3])C(=O)N1CCOCC1) `ZINC001142702724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702724 none CC(C)[C@H](NC(=O)[C@](C)([O-])[SiH3])C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 14, 30, 5, 14, 5, 1, 5, 1, 1, 1, 14, 32, 32, 43, 43, 43, 43, 43, 31, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [6, 8, 9, 10, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 206 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702724 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702724 Building ZINC001142702819 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702819 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/700 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(NC(=O)[C@](C)([O-])[SiH3])CCS(=O)(=O)CC1) `ZINC001142702819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142702819 none COCCC1(NC(=O)[C@](C)([O-])[SiH3])CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 42, 24, 13, 5, 1, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 46, 46, 41, 42, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [6, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 189 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/701 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(NC(=O)[C@@](C)([O-])[SiH3])CCS(=O)(=O)CC1) `ZINC001142702819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142702819 none COCCC1(NC(=O)[C@@](C)([O-])[SiH3])CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 43, 24, 13, 5, 1, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 48, 48, 42, 43, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [6, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702819 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 Building ZINC001142702819 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702819 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 700) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(NC(=O)[C@](C)([O-])[SiH3])CCS(=O)(=O)CC1) `ZINC001142702819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142702819 none COCCC1(NC(=O)[C@](C)([O-])[SiH3])CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 42, 24, 13, 5, 1, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 46, 46, 41, 42, 5, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [6, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 189 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 701) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(NC(=O)[C@@](C)([O-])[SiH3])CCS(=O)(=O)CC1) `ZINC001142702819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 4 8 3 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142702819 none COCCC1(NC(=O)[C@@](C)([O-])[SiH3])CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 43, 24, 13, 5, 1, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 50, 50, 50, 48, 48, 42, 43, 5, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [6, 8, 9, 10, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702819 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702819 Building ZINC001142702829 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702829 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/702 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001142702829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702829 none C[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 21, 39, 39, 39, 39, 50, 50, 50, 39, 39, 1, 1, 1, 5, 17, 17, 39, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/703 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001142702829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702829 none C[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 21, 38, 38, 38, 38, 50, 50, 50, 38, 38, 1, 1, 1, 5, 17, 17, 38, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702829 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 Building ZINC001142702829 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702829 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 702) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001142702829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702829 none C[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 21, 39, 39, 39, 39, 50, 50, 50, 39, 39, 1, 1, 1, 5, 17, 17, 39, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([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]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 703) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001142702829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142702829 none C[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 21, 38, 38, 38, 38, 50, 50, 50, 38, 38, 1, 1, 1, 5, 17, 17, 38, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([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]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702829 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702829 Building ZINC001142702952 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702952 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/704 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(N)CCN(C(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142702952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702952 none CCOC(=O)CC1(N)CCN(C(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 24, 46, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 11, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/705 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(N)CCN(C(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142702952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702952 none CCOC(=O)CC1(N)CCN(C(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 22, 46, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 22, 22, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 11, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702952 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 Building ZINC001142702952 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702952 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 704) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(N)CCN(C(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142702952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702952 none CCOC(=O)CC1(N)CCN(C(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 24, 46, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 24, 24, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 11, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 705) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CC1(N)CCN(C(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142702952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 4 13 3 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702952 none CCOC(=O)CC1(N)CCN(C(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 22, 46, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 22, 22, 4, 4, 4, 4, 4, 4, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 11, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702952 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702952 Building ZINC001142702983 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702983 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/706 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142702983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702983 none COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 24, 24, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 24, 15, 15, 15, 15, 4, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 31] 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, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/707 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142702983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702983 none COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 24, 24, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 24, 15, 15, 15, 15, 4, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 31] 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, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702983 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 Building ZINC001142702983 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142702983 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 706) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142702983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142702983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702983 none COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 24, 24, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 24, 15, 15, 15, 15, 4, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 31] 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, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 707) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142702983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142702983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 4 15 3 19 to be deleted 20 to be deleted 21 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142702983 none COCC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 24, 24, 15, 15, 15, 15, 15, 7, 15, 4, 1, 4, 1, 1, 1, 15, 15, 50, 50, 50, 50, 50, 24, 15, 15, 15, 15, 4, 1, 1, 1, 15, 15, 15, 15] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 31] 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, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142702983 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142702983 Building ZINC001142703064 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703064 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/708 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142703064 none COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 8, 17, 3, 8, 8, 20, 29, 40, 40, 40, 40, 40, 3, 1, 3, 1, 1, 1, 17, 17, 17, 22, 22, 27, 29, 40, 40, 40, 40, 40, 3, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/709 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142703064 none COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 9, 18, 4, 9, 9, 17, 26, 36, 36, 36, 36, 36, 4, 1, 4, 1, 1, 1, 18, 18, 18, 20, 20, 24, 26, 36, 36, 36, 36, 36, 4, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703064 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 Building ZINC001142703064 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703064 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 708) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142703064 none COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 8, 17, 3, 8, 8, 20, 29, 40, 40, 40, 40, 40, 3, 1, 3, 1, 1, 1, 17, 17, 17, 22, 22, 27, 29, 40, 40, 40, 40, 40, 3, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 709) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001142703064 none COC(=O)[C@H](CCc1cn(C)cn1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 9, 18, 4, 9, 9, 17, 26, 36, 36, 36, 36, 36, 4, 1, 4, 1, 1, 1, 18, 18, 18, 20, 20, 24, 26, 36, 36, 36, 36, 36, 4, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703064 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703064 Building ZINC001142703183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/710 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/711 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/712 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/712' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/713 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/713' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 Building ZINC001142703183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 710) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 711) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 712) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 713) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 Building ZINC001142703183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 710) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 711) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 712) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 713) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 Building ZINC001142703183 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142703183 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 710) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 711) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 712) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1) `ZINC001142703183.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 713) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1) `ZINC001142703183.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142703183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 4 9 3 13 to be deleted 14 to be deleted 15 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142703183 none CCOC(=O)[C@]1(NC(=O)[C@](C)([O-])[SiH3])CC[N@](C)CC1 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', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 5, 12, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 22, 40, 3, 3, 1, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 3, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [7, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703183 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703183 Building ZINC001142703231 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703231 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/714 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703231 none COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 4, 13, 13, 22, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 25, 25, 25, 22, 22, 32, 32, 32, 32, 32, 4, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/715 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703231 none COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 4, 13, 13, 20, 28, 28, 28, 28, 28, 4, 1, 4, 1, 1, 1, 26, 26, 26, 20, 20, 28, 28, 28, 28, 28, 4, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703231 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 Building ZINC001142703231 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703231 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 714) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703231 none COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 4, 13, 13, 22, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 25, 25, 25, 22, 22, 32, 32, 32, 32, 32, 4, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 715) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703231 none COC(=O)[C@@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 26, 4, 13, 13, 20, 28, 28, 28, 28, 28, 4, 1, 4, 1, 1, 1, 26, 26, 26, 20, 20, 28, 28, 28, 28, 28, 4, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703231 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703231 Building ZINC001142703232 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703232 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/716 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703232 none COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 16, 28, 5, 16, 16, 24, 32, 32, 32, 32, 32, 5, 1, 5, 1, 1, 1, 28, 28, 28, 24, 24, 32, 32, 32, 32, 32, 5, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/717 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703232 none COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 4, 13, 13, 22, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 25, 25, 25, 22, 22, 32, 32, 32, 32, 32, 4, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703232 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 Building ZINC001142703232 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703232 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 716) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703232 none COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 16, 28, 5, 16, 16, 24, 32, 32, 32, 32, 32, 5, 1, 5, 1, 1, 1, 28, 28, 28, 24, 24, 32, 32, 32, 32, 32, 5, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 717) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703232 none COC(=O)[C@H](Cc1cncn1C)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 5, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 13, 25, 4, 13, 13, 22, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 25, 25, 25, 22, 22, 32, 32, 32, 32, 32, 4, 1, 1, 1] 50 rigid atoms, others: [32, 14, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703232 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703232 Building ZINC001142703263 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703263 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/718 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703263 none COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@](C)([O-])[SiH3] 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 11, 21, 4, 11, 11, 20, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 21, 21, 21, 20, 20, 32, 32, 32, 32, 4, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/719 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703263 none COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@@](C)([O-])[SiH3] 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 4, 13, 13, 24, 36, 36, 36, 36, 36, 4, 1, 4, 1, 1, 1, 19, 19, 19, 24, 24, 36, 36, 36, 36, 4, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703263 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 Building ZINC001142703263 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703263 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 718) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703263 none COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@](C)([O-])[SiH3] 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 11, 21, 4, 11, 11, 20, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 21, 21, 21, 20, 20, 32, 32, 32, 32, 4, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 719) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703263 none COC(=O)[C@@H](Cc1cccnc1)NC(=O)[C@@](C)([O-])[SiH3] 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', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 19, 4, 13, 13, 24, 36, 36, 36, 36, 36, 4, 1, 4, 1, 1, 1, 19, 19, 19, 24, 24, 36, 36, 36, 36, 4, 1, 1, 1] 50 rigid atoms, others: [14, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703263 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703263 Building ZINC001142703292 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703292 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/720 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142703292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142703292 none CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 19, 19, 19, 11, 11, 11, 11, 11, 5, 11, 4, 1, 4, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 48, 48, 19, 11, 11, 11, 11, 4, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/721 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142703292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142703292 none CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 18, 18, 18, 11, 11, 11, 11, 11, 5, 11, 4, 1, 4, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 47, 47, 18, 11, 11, 11, 11, 4, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703292 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 Building ZINC001142703292 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703292 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 720) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1) `ZINC001142703292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142703292 none CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 19, 19, 19, 11, 11, 11, 11, 11, 5, 11, 4, 1, 4, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 48, 48, 19, 11, 11, 11, 11, 4, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 721) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1) `ZINC001142703292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 4 16 3 20 to be deleted 21 to be deleted 22 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001142703292 none CN(C)CC(=O)N[C@H]1CC[C@H](NC(=O)[C@](C)([O-])[SiH3])CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 18, 18, 18, 11, 11, 11, 11, 11, 5, 11, 4, 1, 4, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50, 47, 47, 18, 11, 11, 11, 11, 4, 1, 1, 1, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 14, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703292 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703292 Building ZINC001142703367 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703367 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/722 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1) `ZINC001142703367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142703367 none C[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 8, 8, 8, 20, 20, 20, 21, 39, 50, 50, 42, 50, 50, 1, 1, 1, 3, 5, 5, 8, 20, 20, 39, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/723 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1) `ZINC001142703367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142703367 none C[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 8, 8, 8, 20, 20, 20, 20, 39, 50, 50, 39, 50, 50, 1, 1, 1, 3, 5, 5, 8, 20, 20, 39, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703367 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 Building ZINC001142703367 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703367 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 722) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1) `ZINC001142703367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142703367 none C[C@@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 8, 8, 8, 20, 20, 20, 21, 39, 50, 50, 42, 50, 50, 1, 1, 1, 3, 5, 5, 8, 20, 20, 39, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 723) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1) `ZINC001142703367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142703367 none C[C@]([O-])([SiH3])C(=O)NCC(=O)NCC(=O)OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 11, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 5, 8, 8, 8, 20, 20, 20, 20, 39, 50, 50, 39, 50, 50, 1, 1, 1, 3, 5, 5, 8, 20, 20, 39, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 21, 22, 23] set([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]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703367 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703367 Building ZINC001142703418 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703418 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/724 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O) `ZINC001142703418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703418 none C[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 11, 18, 38, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 2, 11, 11, 18, 18, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/725 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O) `ZINC001142703418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703418 none C[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 11, 18, 38, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 2, 11, 11, 18, 18, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703418 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 Building ZINC001142703418 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703418 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 724) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O) `ZINC001142703418.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703418 none C[C@@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 11, 18, 38, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 2, 11, 11, 18, 18, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 725) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O) `ZINC001142703418.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 1 is the cov attach 4 1 0 4 1 1 4 1 2 3 1 2 4 to be deleted 5 to be deleted 6 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142703418 none C[C@]([O-])([SiH3])C(=O)NCCOc1ccccc1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 11, 18, 38, 49, 49, 49, 49, 49, 49, 50, 50, 1, 1, 1, 2, 11, 11, 18, 18, 49, 49, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703418 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703418 Building ZINC001142703595 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703595 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/726 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703595 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 32, 31, 17, 31, 6, 17, 17, 29, 34, 34, 34, 34, 34, 6, 1, 6, 1, 1, 1, 40, 40, 40, 40, 40, 29, 29, 34, 34, 6, 1, 1, 1] 50 rigid atoms, others: [32, 15, 17, 18, 19, 30, 31] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/727 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703595 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 34, 32, 17, 32, 5, 17, 17, 30, 35, 35, 35, 35, 35, 5, 1, 5, 1, 1, 1, 44, 44, 44, 44, 44, 30, 30, 35, 35, 5, 1, 1, 1] 50 rigid atoms, others: [32, 15, 17, 18, 19, 30, 31] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703595 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 Building ZINC001142703595 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703595 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 726) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@](C)([O-])[SiH3]) `ZINC001142703595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703595 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 32, 31, 17, 31, 6, 17, 17, 29, 34, 34, 34, 34, 34, 6, 1, 6, 1, 1, 1, 40, 40, 40, 40, 40, 29, 29, 34, 34, 6, 1, 1, 1] 50 rigid atoms, others: [32, 15, 17, 18, 19, 30, 31] 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]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 727) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@](C)([O-])[SiH3]) `ZINC001142703595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 4 17 3 21 to be deleted 22 to be deleted 23 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703595 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@](C)([O-])[SiH3] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 34, 32, 17, 32, 5, 17, 17, 30, 35, 35, 35, 35, 35, 5, 1, 5, 1, 1, 1, 44, 44, 44, 44, 44, 30, 30, 35, 35, 5, 1, 1, 1] 50 rigid atoms, others: [32, 15, 17, 18, 19, 30, 31] 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]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703595 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703595 Building ZINC001142703651 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703651 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/728 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1nccc(CNC(=O)[C@](C)([O-])[SiH3])n1) `ZINC001142703651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703651 none COCCOc1nccc(CNC(=O)[C@](C)([O-])[SiH3])n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 5, 8, 1, 11, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 34, 12, 12, 12, 12, 12, 9, 2, 2, 1, 2, 1, 1, 1, 12, 50, 50, 50, 50, 50, 47, 47, 12, 12, 9, 9, 2, 1, 1, 1] 50 rigid atoms, others: [32, 12, 14, 15, 16, 30, 31] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/729 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1nccc(CNC(=O)[C@@](C)([O-])[SiH3])n1) `ZINC001142703651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703651 none COCCOc1nccc(CNC(=O)[C@@](C)([O-])[SiH3])n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 5, 8, 1, 11, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 33, 12, 12, 12, 12, 12, 9, 2, 2, 1, 2, 1, 1, 1, 12, 50, 50, 50, 50, 50, 47, 47, 12, 12, 9, 9, 2, 1, 1, 1] 50 rigid atoms, others: [32, 12, 14, 15, 16, 30, 31] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703651 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 Building ZINC001142703651 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142703651 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 728) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1nccc(CNC(=O)[C@](C)([O-])[SiH3])n1) `ZINC001142703651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142703651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703651 none COCCOc1nccc(CNC(=O)[C@](C)([O-])[SiH3])n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 5, 8, 1, 11, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 34, 12, 12, 12, 12, 12, 9, 2, 2, 1, 2, 1, 1, 1, 12, 50, 50, 50, 50, 50, 47, 47, 12, 12, 9, 9, 2, 1, 1, 1] 50 rigid atoms, others: [32, 12, 14, 15, 16, 30, 31] 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 729) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOc1nccc(CNC(=O)[C@@](C)([O-])[SiH3])n1) `ZINC001142703651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142703651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 4 14 3 18 to be deleted 19 to be deleted 20 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142703651 none COCCOc1nccc(CNC(=O)[C@@](C)([O-])[SiH3])n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 5, 8, 1, 11, 5, 5, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 47, 33, 12, 12, 12, 12, 12, 9, 2, 2, 1, 2, 1, 1, 1, 12, 50, 50, 50, 50, 50, 47, 47, 12, 12, 9, 9, 2, 1, 1, 1] 50 rigid atoms, others: [32, 12, 14, 15, 16, 30, 31] 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001142703651 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001142703651 Building ZINC001143950971 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143950971 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/730 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001143950971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143950971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950971 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 13, 18, 18, 18, 18, 38, 42, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/731 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001143950971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143950971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950971 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 13, 22, 22, 19, 22, 41, 45, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143950971 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 Building ZINC001143950971 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143950971 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 730) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001143950971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143950971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950971 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 13, 18, 18, 18, 18, 38, 42, 50, 50, 50, 50, 50, 18, 18, 1, 1, 1, 1, 1, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 731) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1) `ZINC001143950971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143950971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950971 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 13, 22, 22, 19, 22, 41, 45, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143950971 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950971 Building ZINC001143950972 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143950972 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/732 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001143950972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143950972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950972 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 15, 19, 19, 19, 19, 36, 42, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/733 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001143950972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143950972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950972 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 13, 22, 22, 20, 22, 41, 45, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143950972 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 Building ZINC001143950972 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143950972 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 732) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001143950972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143950972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950972 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 15, 19, 19, 19, 19, 36, 42, 50, 50, 50, 50, 50, 19, 19, 1, 1, 1, 1, 1, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 733) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1) `ZINC001143950972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143950972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143950972 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)[C@@H]2CCCO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 13, 22, 22, 20, 22, 41, 45, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 128 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143950972 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143950972 Building ZINC001143959134 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959134 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/734 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1) `ZINC001143959134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143959134 none CC[C@@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 42, 42, 42, 16, 1, 1, 1, 1, 1, 4, 16, 16, 42, 42, 16] 42 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/735 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1) `ZINC001143959134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143959134 none CC[C@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 42, 42, 42, 16, 1, 1, 1, 1, 1, 4, 16, 16, 42, 42, 16] 42 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959134 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 Building ZINC001143959134 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959134 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 734) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1) `ZINC001143959134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143959134 none CC[C@@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 42, 42, 42, 16, 1, 1, 1, 1, 1, 4, 16, 16, 42, 42, 16] 42 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 735) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1) `ZINC001143959134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143959134 none CC[C@]([O-])([SiH3])C(=O)Nc1cncc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 42, 42, 42, 16, 1, 1, 1, 1, 1, 4, 16, 16, 42, 42, 16] 42 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959134 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959134 Building ZINC001143959387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/736 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@]([O-])([SiH3])CC)C2) `ZINC001143959387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959387 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@]([O-])([SiH3])CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 8, 37, 8, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/737 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@]([O-])([SiH3])CC)C2) `ZINC001143959387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959387 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@]([O-])([SiH3])CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 8, 36, 8, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 Building ZINC001143959387 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959387 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 736) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@]([O-])([SiH3])CC)C2) `ZINC001143959387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959387 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@]([O-])([SiH3])CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 8, 37, 8, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 737) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@]([O-])([SiH3])CC)C2) `ZINC001143959387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959387 none CCOC(=O)c1nc2n(n1)CCN(C(=O)[C@@]([O-])([SiH3])CC)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 8, 36, 8, 8, 8, 8, 8, 8, 8, 3, 1, 6, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [32, 33, 13, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959387 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959387 Building ZINC001143959526 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959526 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/738 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001143959526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959526 none CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 25, 34, 34, 34, 34, 32, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/739 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001143959526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959526 none CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 22, 32, 32, 32, 32, 28, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 31, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959526 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 Building ZINC001143959526 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959526 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 738) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001143959526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959526 none CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 25, 34, 34, 34, 34, 32, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 739) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001143959526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959526 none CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_NAME dock atom types: ['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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 22, 32, 32, 32, 32, 28, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 31, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959526 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959526 Building ZINC001143959589 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959589 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/740 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/741 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/742 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/742' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/743 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/743' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959589 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 Building ZINC001143959589 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959589 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 740) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 741) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 742) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 743) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959589 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 Building ZINC001143959589 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959589 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 740) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 741) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 742) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 743) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959589 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 Building ZINC001143959589 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959589 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 740) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 741) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 742) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 10, 28, 28, 28, 28, 28, 27, 28, 28, 28, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 743) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1) `ZINC001143959589.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959589 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1cnccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 12, 29, 29, 29, 29, 29, 28, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959589 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959589 Building ZINC001143959593 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959593 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/744 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1) `ZINC001143959593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143959593 none CC[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 10, 10] 20 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/745 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1) `ZINC001143959593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143959593 none CC[C@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12] 26 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959593 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 Building ZINC001143959593 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959593 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 744) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1) `ZINC001143959593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143959593 none CC[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 20, 10, 10] 20 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 745) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1) `ZINC001143959593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143959593 none CC[C@]([O-])([SiH3])C(=O)N1CC[C@H]2OCC[C@@H](C(=O)NC)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 26, 12, 12] 26 rigid atoms, others: [0, 1, 2, 3, 23, 24, 25, 26, 27] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959593 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959593 Building ZINC001143959609 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959609 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/746 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001143959609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143959609 none CC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 33, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 33, 33, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/747 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001143959609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143959609 none CC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 30, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 30, 30, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959609 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 Building ZINC001143959609 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959609 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 746) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001143959609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143959609 none CC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 8, 33, 50, 50, 50, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 33, 33, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 747) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001143959609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143959609 none CC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 6, 30, 50, 50, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 30, 30, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959609 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959609 Building ZINC001143959657 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959657 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/748 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])CC)c(C(N)=O)nn1C) `ZINC001143959657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143959657 none CCc1c(NC(=O)[C@@]([O-])([SiH3])CC)c(C(N)=O)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 8, 11, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 4, 4, 1, 4, 1, 1, 1, 1, 19, 19, 40, 40, 19, 19, 19, 26, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 40, 40, 19, 19, 19] 50 rigid atoms, others: [5, 7, 8, 9, 10, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/749 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])CC)c(C(N)=O)nn1C) `ZINC001143959657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143959657 none CCc1c(NC(=O)[C@]([O-])([SiH3])CC)c(C(N)=O)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 8, 11, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 4, 4, 1, 4, 1, 1, 1, 1, 19, 19, 40, 40, 19, 19, 19, 26, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 40, 40, 19, 19, 19] 50 rigid atoms, others: [5, 7, 8, 9, 10, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959657 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 Building ZINC001143959657 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959657 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 748) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@@]([O-])([SiH3])CC)c(C(N)=O)nn1C) `ZINC001143959657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143959657 none CCc1c(NC(=O)[C@@]([O-])([SiH3])CC)c(C(N)=O)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 8, 11, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 4, 4, 1, 4, 1, 1, 1, 1, 19, 19, 40, 40, 19, 19, 19, 26, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 40, 40, 19, 19, 19] 50 rigid atoms, others: [5, 7, 8, 9, 10, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 749) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(NC(=O)[C@]([O-])([SiH3])CC)c(C(N)=O)nn1C) `ZINC001143959657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143959657 none CCc1c(NC(=O)[C@]([O-])([SiH3])CC)c(C(N)=O)nn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 8, 11, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 19, 19, 4, 4, 1, 4, 1, 1, 1, 1, 19, 19, 40, 40, 19, 19, 19, 26, 26, 26, 26, 26, 4, 1, 1, 1, 1, 1, 40, 40, 19, 19, 19] 50 rigid atoms, others: [5, 7, 8, 9, 10, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959657 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959657 Building ZINC001143959697 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959697 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/750 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001143959697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959697 none CC[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/751 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001143959697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959697 none CC[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 17, 17] 44 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959697 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 Building ZINC001143959697 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959697 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 750) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001143959697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959697 none CC[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 8, 16, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 16, 16, 16, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 751) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21) `ZINC001143959697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959697 none CC[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]2CN(S(C)(=O)=O)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 12, 17, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 44, 44, 44, 17, 17] 44 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959697 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959697 Building ZINC001143959710 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959710 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/752 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1) `ZINC001143959710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143959710 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 45, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 45, 45, 45, 22, 22] 45 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/753 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1) `ZINC001143959710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143959710 none CC[C@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 21, 21, 21, 21, 21, 21, 21, 21, 43, 43, 43, 21, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 43, 43, 43, 21, 21] 43 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959710 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 Building ZINC001143959710 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959710 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 752) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1) `ZINC001143959710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143959710 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 22, 22, 22, 22, 22, 22, 22, 22, 45, 45, 45, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 45, 45, 45, 22, 22] 45 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 123 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 753) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1) `ZINC001143959710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143959710 none CC[C@]([O-])([SiH3])C(=O)N1C[C@H]2COC[C@@]2(C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 21, 21, 21, 21, 21, 21, 21, 21, 43, 43, 43, 21, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 43, 43, 43, 21, 21] 43 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959710 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959710 Building ZINC001143959716 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959716 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/754 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/755 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/756 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/756' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/757 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/757' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959716 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 Building ZINC001143959716 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959716 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 754) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 755) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 756) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 757) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959716 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 Building ZINC001143959716 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959716 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 754) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 755) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 756) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 757) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959716 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 Building ZINC001143959716 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143959716 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 754) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 755) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 756) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 36, 36, 29, 36, 36, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 36, 29, 36] 36 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 757) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1) `ZINC001143959716.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143959716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143959716 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2[C@H](C1)OCCN2c1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 12, 5, 5, 8, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 11, 26, 26, 26, 26, 26, 25, 26, 26, 26, 26, 26, 39, 39, 26, 39, 39, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 39, 26, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959716 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959716 Building ZINC001143959844 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959844 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/758 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001143959844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959844 none CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 8, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/759 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001143959844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959844 none CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 9, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959844 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 Building ZINC001143959844 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959844 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 758) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001143959844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959844 none CC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 8, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 759) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001143959844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143959844 none CC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 9, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 37 rigid atoms, others: [0, 1, 2, 3, 18, 19, 20, 21, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959844 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959844 Building ZINC001143959921 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959921 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/760 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001143959921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001143959921 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 29, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/761 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001143959921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001143959921 none CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959921 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 Building ZINC001143959921 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959921 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 760) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001143959921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001143959921 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 5, 7, 7, 7, 7, 29, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 761) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1) `ZINC001143959921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001143959921 none CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)N2CCCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 27, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143959921 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143959921 Building ZINC001143960036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/762 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC) `ZINC001143960036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960036 none CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 14, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/763 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC) `ZINC001143960036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960036 none CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 14, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 3, 3, 6, 6, 6] 12 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 Building ZINC001143960036 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960036 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 762) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC) `ZINC001143960036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960036 none CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 14, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 13 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 763) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC) `ZINC001143960036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960036 none CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)SC[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 14, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 6, 6, 6, 1, 1, 1, 1, 1, 5, 5, 5, 3, 3, 6, 6, 6] 12 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960036 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960036 Building ZINC001143960037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/764 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC) `ZINC001143960037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960037 none CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 9, 9, 9, 1, 1, 1, 1, 1, 11, 11, 11, 4, 4, 9, 9, 9] 22 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/765 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC) `ZINC001143960037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960037 none CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 2, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 2, 2, 6, 6, 6] 11 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 Building ZINC001143960037 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960037 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 764) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC) `ZINC001143960037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960037 none CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 9, 9, 9, 1, 1, 1, 1, 1, 11, 11, 11, 4, 4, 9, 9, 9] 22 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 765) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC) `ZINC001143960037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960037 none CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 2, 2, 2, 2, 2, 6, 6, 6, 1, 1, 1, 1, 1, 4, 4, 4, 2, 2, 6, 6, 6] 11 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960037 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960037 Building ZINC001143960038 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960038 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/766 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960038 none CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 2, 2, 2, 2, 2, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 2, 2, 6, 6, 6] 16 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/767 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960038 none CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 9, 9, 9, 1, 1, 1, 1, 1, 11, 11, 11, 4, 4, 9, 9, 9] 21 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960038 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 Building ZINC001143960038 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960038 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 766) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960038 none CC[C@@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 6, 2, 2, 2, 2, 2, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 2, 2, 6, 6, 6] 16 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 767) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960038 none CC[C@]([O-])([SiH3])C(=O)N1[C@@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 11, 11, 11, 4, 4, 4, 4, 4, 9, 9, 9, 1, 1, 1, 1, 1, 11, 11, 11, 4, 4, 9, 9, 9] 21 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960038 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960038 Building ZINC001143960039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/768 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960039 none CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 7, 7, 7, 1, 1, 1, 1, 1, 9, 9, 9, 5, 5, 7, 7, 7] 14 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/769 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960039 none CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 Building ZINC001143960039 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960039 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 768) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960039 none CC[C@@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 7, 7, 7, 1, 1, 1, 1, 1, 9, 9, 9, 5, 5, 7, 7, 7] 14 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 769) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC) `ZINC001143960039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960039 none CC[C@]([O-])([SiH3])C(=O)N1[C@H](C(=O)OC)CS[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 12, 5, 5, 14, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4] 4 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960039 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960039 Building ZINC001143960098 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960098 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/770 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001143960098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960098 none CC[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 37, 37, 37, 13, 14, 14, 14, 1, 1, 1, 1, 1, 6, 14, 37, 37, 14, 14, 14, 14] 37 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/771 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001143960098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960098 none CC[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 37, 37, 37, 14, 14, 14, 14, 1, 1, 1, 1, 1, 6, 14, 37, 37, 14, 14, 14, 14] 37 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960098 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 Building ZINC001143960098 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960098 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 770) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001143960098.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960098 none CC[C@@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 37, 37, 37, 13, 14, 14, 14, 1, 1, 1, 1, 1, 6, 14, 37, 37, 14, 14, 14, 14] 37 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 771) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N) `ZINC001143960098.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960098 none CC[C@]([O-])([SiH3])C(=O)Nc1cc(S(N)(=O)=O)ccc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 37, 37, 37, 14, 14, 14, 14, 1, 1, 1, 1, 1, 6, 14, 37, 37, 14, 14, 14, 14] 37 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960098 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960098 Building ZINC001143960148 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960148 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/772 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001143960148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143960148 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 15, 22, 30, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 22, 22, 30, 30, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/773 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001143960148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143960148 none CC[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 11, 17, 27, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 17, 17, 27, 27, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960148 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 Building ZINC001143960148 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960148 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 772) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001143960148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143960148 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 15, 22, 30, 50, 50, 50, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 22, 22, 30, 30, 50, 50, 50, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 773) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1) `ZINC001143960148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143960148 none CC[C@]([O-])([SiH3])C(=O)N1CCN(CCCS(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 11, 17, 27, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 17, 17, 27, 27, 50, 50, 50, 4, 4, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 241 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960148 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960148 Building ZINC001143960164 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960164 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/774 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1) `ZINC001143960164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960164 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 19, 19, 19, 19, 19, 19, 19, 40, 40, 40, 40, 40, 19, 19, 19, 19, 1, 1, 1, 1, 1, 19, 19, 40, 40, 40, 40, 40, 19, 19, 19, 19] 40 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/775 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1) `ZINC001143960164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960164 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 10, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960164 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 Building ZINC001143960164 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960164 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 774) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1) `ZINC001143960164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960164 none CC[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 9, 19, 19, 19, 19, 19, 19, 19, 40, 40, 40, 40, 40, 19, 19, 19, 19, 1, 1, 1, 1, 1, 19, 19, 40, 40, 40, 40, 40, 19, 19, 19, 19] 40 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 775) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1) `ZINC001143960164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960164 none CC[C@]([O-])([SiH3])C(=O)N1C[C@@H]2C(=O)N(c3cnn(C)c3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 10, 20, 20, 20, 20, 20, 20, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960164 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960164 Building ZINC001143960174 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960174 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/776 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1) `ZINC001143960174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143960174 none CC[C@@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 21, 31, 31, 31, 50, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 21, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/777 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1) `ZINC001143960174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143960174 none CC[C@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 21, 30, 30, 30, 50, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 21, 50, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960174 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 Building ZINC001143960174 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960174 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 776) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1) `ZINC001143960174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143960174 none CC[C@@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 21, 31, 31, 31, 50, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 21, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 777) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1) `ZINC001143960174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143960174 none CC[C@]([O-])([SiH3])C(=O)N1CCC(NS(=O)(=O)CC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 21, 30, 30, 30, 50, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 21, 50, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960174 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960174 Building ZINC001143960262 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960262 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/778 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001143960262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960262 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 12, 15, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/779 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001143960262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960262 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 11, 16, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960262 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 Building ZINC001143960262 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960262 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 778) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001143960262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960262 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 12, 15, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 126 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 779) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1) `ZINC001143960262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143960262 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C2CCOCC2)C(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 12, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 11, 16, 17, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960262 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960262 Building ZINC001143960421 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960421 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/780 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1) `ZINC001143960421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143960421 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 26, 49, 49, 49, 50, 50, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 49, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/781 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1) `ZINC001143960421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143960421 none CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 23, 49, 49, 49, 50, 50, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 49, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960421 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 Building ZINC001143960421 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960421 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 780) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1) `ZINC001143960421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143960421 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 4, 8, 8, 8, 8, 26, 49, 49, 49, 50, 50, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 26, 26, 49, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 781) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1) `ZINC001143960421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001143960421 none CC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)NC(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 3, 7, 7, 7, 7, 23, 49, 49, 49, 50, 50, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 23, 23, 49, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960421 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960421 Building ZINC001143960471 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960471 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/782 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC) `ZINC001143960471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960471 none CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 20, 49, 8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 50, 50, 50, 50, 50, 20, 20, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/783 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC) `ZINC001143960471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960471 none CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 19, 48, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 1, 50, 50, 50, 50, 50, 19, 19, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960471 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 Building ZINC001143960471 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960471 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 782) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC) `ZINC001143960471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960471 none CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 20, 49, 8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 1, 50, 50, 50, 50, 50, 20, 20, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 783) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC) `ZINC001143960471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960471 none CCOC(=O)C[C@@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 19, 48, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 1, 50, 50, 50, 50, 50, 19, 19, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960471 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960471 Building ZINC001143960472 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960472 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/784 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC) `ZINC001143960472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960472 none CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 50, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 1, 50, 50, 50, 50, 50, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/785 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC) `ZINC001143960472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960472 none CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 18, 49, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 1, 50, 50, 50, 50, 50, 18, 18, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960472 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 Building ZINC001143960472 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960472 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 784) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC) `ZINC001143960472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960472 none CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 20, 50, 7, 7, 7, 7, 7, 7, 7, 7, 6, 2, 6, 1, 1, 1, 1, 50, 50, 50, 50, 50, 20, 20, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 785) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC) `ZINC001143960472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143960472 none CCOC(=O)C[C@H]1C(=O)NCCN1C(=O)[C@@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 6, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 18, 49, 6, 6, 6, 6, 6, 6, 6, 6, 5, 2, 5, 1, 1, 1, 1, 50, 50, 50, 50, 50, 18, 18, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960472 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960472 Building ZINC001143960616 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960616 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/786 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1) `ZINC001143960616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960616 none CC[C@@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 11, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10] 34 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/787 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1) `ZINC001143960616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960616 none CC[C@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 11, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10] 34 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960616 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 Building ZINC001143960616 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960616 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 786) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1) `ZINC001143960616.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960616 none CC[C@@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 11, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10] 34 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 787) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1) `ZINC001143960616.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001143960616 none CC[C@]([O-])([SiH3])C(=O)N1CCn2cc(C(=O)OC)nc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 11, 12, 5, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 10, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10, 10, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 34, 34, 34, 10, 10] 34 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960616 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960616 Building ZINC001143960620 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960620 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/788 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1) `ZINC001143960620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960620 none CC[C@@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 12, 8, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 8, 8] 32 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/789 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1) `ZINC001143960620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960620 none CC[C@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 12, 8, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 8, 8] 32 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960620 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 Building ZINC001143960620 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960620 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 788) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1) `ZINC001143960620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960620 none CC[C@@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 12, 8, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 8, 8] 32 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 789) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1) `ZINC001143960620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143960620 none CC[C@]([O-])([SiH3])C(=O)N1CCc2nc(O)nc(O)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 12, 8, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 4, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 8, 8] 32 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960620 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960620 Building ZINC001143960920 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960920 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/790 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO) `ZINC001143960920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960920 none CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 63] 63 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/791 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO) `ZINC001143960920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960920 none CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 25, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 25, 25, 75] 75 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 161 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960920 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 Building ZINC001143960920 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960920 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 790) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO) `ZINC001143960920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960920 none CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 63] 63 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 791) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO) `ZINC001143960920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960920 none CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 25, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 25, 25, 75] 75 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 161 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960920 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960920 Building ZINC001143960921 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960921 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/792 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO) `ZINC001143960921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960921 none CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 25, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 75] 75 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/793 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO) `ZINC001143960921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960921 none CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 63] 63 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960921 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 Building ZINC001143960921 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143960921 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 792) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO) `ZINC001143960921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143960921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960921 none CC[C@@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 25, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 75] 75 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 793) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO) `ZINC001143960921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143960921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143960921 none CC[C@]([O-])([SiH3])C(=O)N1Cc2ccnn2CC[C@@H]1CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 9, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 63] 63 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143960921 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143960921 Building ZINC001143961111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/794 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001143961111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143961111 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 8, 15, 20, 20, 20, 20, 27, 27, 20, 20, 27, 27, 20, 20, 1, 1, 1, 1, 1, 20, 20, 20, 20, 27, 54, 27, 20, 20, 20, 20] 54 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/795 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001143961111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143961111 none CC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 8, 15, 22, 22, 22, 22, 28, 28, 22, 22, 28, 28, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 28, 56, 28, 22, 22, 22, 22] 56 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 Building ZINC001143961111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 794) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001143961111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143961111 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 8, 15, 20, 20, 20, 20, 27, 27, 20, 20, 27, 27, 20, 20, 1, 1, 1, 1, 1, 20, 20, 20, 20, 27, 54, 27, 20, 20, 20, 20] 54 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 795) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1) `ZINC001143961111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143961111 none CC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncc(O)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 8, 15, 22, 22, 22, 22, 28, 28, 22, 22, 28, 28, 22, 22, 1, 1, 1, 1, 1, 22, 22, 22, 22, 28, 56, 28, 22, 22, 22, 22] 56 rigid atoms, others: [0, 1, 2, 3, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961111 Building ZINC001143961146 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961146 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/796 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001143961146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961146 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 10, 10, 13, 13, 13, 13, 27, 27, 13, 13, 13, 29, 29, 29, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 27, 29, 29, 29, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/797 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001143961146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961146 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 10, 10, 15, 15, 15, 15, 29, 29, 15, 15, 15, 33, 33, 33, 15, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 29, 33, 33, 33, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961146 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 Building ZINC001143961146 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961146 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 796) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001143961146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961146 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 10, 10, 13, 13, 13, 13, 27, 27, 13, 13, 13, 29, 29, 29, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 27, 29, 29, 29, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 797) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001143961146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961146 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 10, 10, 15, 15, 15, 15, 29, 29, 15, 15, 15, 33, 33, 33, 15, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 29, 33, 33, 33, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961146 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961146 Building ZINC001143961147 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961147 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/798 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001143961147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961147 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 24, 24, 12, 12, 12, 29, 29, 29, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 24, 24, 24, 29, 29, 29, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/799 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001143961147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961147 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 27, 27, 13, 13, 13, 28, 28, 28, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 27, 28, 28, 28, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961147 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 Building ZINC001143961147 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961147 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 798) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001143961147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961147 none CC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 8, 8, 12, 12, 12, 12, 24, 24, 12, 12, 12, 29, 29, 29, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12, 24, 24, 24, 29, 29, 29, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 799) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001143961147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001143961147 none CC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 27, 27, 13, 13, 13, 28, 28, 28, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 27, 27, 27, 28, 28, 28, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961147 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961147 Building ZINC001143961149 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961149 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/800 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001143961149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001143961149 none CC[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 38, 38, 38, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/801 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001143961149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001143961149 none CC[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 33, 33, 33, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961149 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 Building ZINC001143961149 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143961149 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 800) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001143961149.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143961149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001143961149 none CC[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 38, 38, 38, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 38, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 801) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1) `ZINC001143961149.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143961149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001143961149 none CC[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)N2CCOCC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 4, 9, 9, 9, 9, 33, 33, 33, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 33, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143961149 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143961149 Building ZINC001143969614 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143969614 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/802 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@]([O-])([SiH3])CC)c(=O)n(CC)c1=O) `ZINC001143969614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143969614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143969614 none CCn1c(N)c(NC(=O)[C@]([O-])([SiH3])CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 7, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [32, 7, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/803 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@@]([O-])([SiH3])CC)c(=O)n(CC)c1=O) `ZINC001143969614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143969614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143969614 none CCn1c(N)c(NC(=O)[C@@]([O-])([SiH3])CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 7, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [32, 7, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143969614 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 Building ZINC001143969614 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143969614 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 802) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@]([O-])([SiH3])CC)c(=O)n(CC)c1=O) `ZINC001143969614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143969614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143969614 none CCn1c(N)c(NC(=O)[C@]([O-])([SiH3])CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 7, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [32, 7, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 803) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(N)c(NC(=O)[C@@]([O-])([SiH3])CC)c(=O)n(CC)c1=O) `ZINC001143969614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143969614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143969614 none CCn1c(N)c(NC(=O)[C@@]([O-])([SiH3])CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.pl3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 13, 13, 13, 13, 26, 13, 13, 25, 25, 25, 25, 25, 13, 13, 7, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26] 50 rigid atoms, others: [32, 7, 9, 10, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143969614 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143969614 Building ZINC001143971435 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971435 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/804 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001143971435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001143971435 none CC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 16, 37, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 16, 37, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/805 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001143971435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001143971435 none CC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 14, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 1, 1, 1, 1, 1, 14, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971435 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 Building ZINC001143971435 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971435 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 804) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001143971435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001143971435 none CC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 16, 37, 37, 37, 37, 37, 37, 37, 37, 50, 50, 50, 1, 1, 1, 1, 1, 16, 37, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 805) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001143971435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001143971435 none CC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 14, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 1, 1, 1, 1, 1, 14, 28, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971435 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971435 Building ZINC001143971703 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971703 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/806 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN) `ZINC001143971703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971703 none CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 20, 32, 32, 32, 32, 32, 49, 49, 32, 32, 32, 32, 37, 1, 1, 1, 1, 1, 3, 14, 14, 49, 49, 49, 49, 49, 49, 49, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/807 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN) `ZINC001143971703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971703 none CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 18, 33, 33, 33, 33, 33, 48, 48, 33, 33, 33, 33, 37, 1, 1, 1, 1, 1, 2, 13, 13, 48, 48, 48, 48, 48, 48, 48, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971703 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 Building ZINC001143971703 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971703 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 806) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN) `ZINC001143971703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971703 none CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 20, 32, 32, 32, 32, 32, 49, 49, 32, 32, 32, 32, 37, 1, 1, 1, 1, 1, 3, 14, 14, 49, 49, 49, 49, 49, 49, 49, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 807) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN) `ZINC001143971703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971703 none CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 18, 33, 33, 33, 33, 33, 48, 48, 33, 33, 33, 33, 37, 1, 1, 1, 1, 1, 2, 13, 13, 48, 48, 48, 48, 48, 48, 48, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971703 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971703 Building ZINC001143971704 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971704 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/808 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN) `ZINC001143971704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971704 none CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 19, 31, 31, 31, 31, 31, 49, 49, 31, 31, 31, 31, 33, 1, 1, 1, 1, 1, 3, 14, 14, 49, 49, 49, 49, 49, 49, 49, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/809 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN) `ZINC001143971704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971704 none CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 17, 33, 33, 33, 33, 33, 48, 48, 33, 33, 33, 33, 36, 1, 1, 1, 1, 1, 2, 11, 11, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971704 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 Building ZINC001143971704 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971704 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 808) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN) `ZINC001143971704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971704 none CC[C@@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 19, 31, 31, 31, 31, 31, 49, 49, 31, 31, 31, 31, 33, 1, 1, 1, 1, 1, 3, 14, 14, 49, 49, 49, 49, 49, 49, 49, 33, 33, 33, 33] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 809) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN) `ZINC001143971704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001143971704 none CC[C@]([O-])([SiH3])C(=O)NC[C@H]1O[C@@H](C(C)C)O[C@@H]1CN NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 7, 5, 5, 5, 12, 5, 7, 5, 10, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 17, 33, 33, 33, 33, 33, 48, 48, 33, 33, 33, 33, 36, 1, 1, 1, 1, 1, 2, 11, 11, 48, 48, 48, 48, 48, 48, 48, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971704 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971704 Building ZINC001143971753 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971753 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/810 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nnc(CNC(=O)[C@]([O-])([SiH3])CC)o1) `ZINC001143971753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143971753 none CCOC(=O)c1nnc(CNC(=O)[C@]([O-])([SiH3])CC)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 26, 41, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/811 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nnc(CNC(=O)[C@@]([O-])([SiH3])CC)o1) `ZINC001143971753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143971753 none CCOC(=O)c1nnc(CNC(=O)[C@@]([O-])([SiH3])CC)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 26, 41, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971753 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 Building ZINC001143971753 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971753 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 810) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nnc(CNC(=O)[C@]([O-])([SiH3])CC)o1) `ZINC001143971753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143971753 none CCOC(=O)c1nnc(CNC(=O)[C@]([O-])([SiH3])CC)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 26, 41, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 811) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1nnc(CNC(=O)[C@@]([O-])([SiH3])CC)o1) `ZINC001143971753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001143971753 none CCOC(=O)c1nnc(CNC(=O)[C@@]([O-])([SiH3])CC)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 26, 41, 26, 26, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971753 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971753 Building ZINC001143971913 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971913 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/812 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001143971913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143971913 none CC[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 22, 31, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/813 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001143971913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143971913 none CC[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 21, 31, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971913 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 Building ZINC001143971913 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971913 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 812) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001143971913.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143971913 none CC[C@@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 22, 31, 50, 50, 50, 50, 50, 22, 22, 1, 1, 1, 1, 1, 2, 9, 9, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 813) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1) `ZINC001143971913.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143971913 none CC[C@]([O-])([SiH3])C(=O)NCc1ccc(N2CCOCC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 21, 31, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143971913 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143971913 Building ZINC001143972058 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972058 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/814 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2) `ZINC001143972058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001143972058 none CC[C@@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 12, 8, 6, 1, 8, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 36, 36] 108 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/815 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2) `ZINC001143972058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001143972058 none CC[C@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 12, 8, 6, 1, 8, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 7, 39, 39] 117 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972058 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 Building ZINC001143972058 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972058 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 814) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2) `ZINC001143972058.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001143972058 none CC[C@@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 12, 8, 6, 1, 8, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 6, 36, 36] 108 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 815) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2) `ZINC001143972058.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 30 natoms 29 natoms 28 natoms 27 names: ZINC001143972058 none CC[C@]([O-])([SiH3])C(=O)Nc1nc(O)[nH]c2nc(O)nc1-2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'O.3', 'N.pl3', 'H', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 12, 8, 6, 1, 8, 1, 12, 8, 1, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 7, 39, 39] 117 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972058 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972058 Building ZINC001143972119 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972119 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/816 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C) `ZINC001143972119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143972119 none CC[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 31, 33, 48, 48, 48, 48, 48, 10, 25, 25, 1, 1, 1, 1, 1, 3, 48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/817 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C) `ZINC001143972119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143972119 none CC[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 33, 34, 44, 44, 44, 44, 44, 10, 25, 25, 1, 1, 1, 1, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972119 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 Building ZINC001143972119 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972119 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 816) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C) `ZINC001143972119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143972119 none CC[C@@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 31, 33, 48, 48, 48, 48, 48, 10, 25, 25, 1, 1, 1, 1, 1, 3, 48, 48, 48, 48, 48, 48, 48, 48, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 817) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C) `ZINC001143972119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001143972119 none CC[C@]([O-])([SiH3])C(=O)N[C@H](C(=O)N1CCOCC1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 33, 34, 44, 44, 44, 44, 44, 10, 25, 25, 1, 1, 1, 1, 1, 3, 44, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972119 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972119 Building ZINC001143972235 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972235 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/818 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C) `ZINC001143972235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143972235 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 11, 1, 12, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 19, 114, 38, 38, 38] 114 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/819 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C) `ZINC001143972235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143972235 none CC[C@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 11, 1, 12, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 19, 114, 38, 38, 38] 114 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972235 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 Building ZINC001143972235 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972235 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 818) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C) `ZINC001143972235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143972235 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 11, 1, 12, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 19, 114, 38, 38, 38] 114 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 819) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C) `ZINC001143972235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001143972235 none CC[C@]([O-])([SiH3])C(=O)Nc1c(N=O)c(O)nc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'O.2', 'C.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 11, 1, 12, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 19, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 19, 114, 38, 38, 38] 114 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972235 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972235 Building ZINC001143972526 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972526 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/820 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001143972526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143972526 none CC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 2, 2, 2, 12, 16, 35, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 26, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/821 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001143972526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143972526 none CC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 2, 2, 2, 12, 16, 35, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 26, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972526 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 Building ZINC001143972526 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972526 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 820) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001143972526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143972526 none CC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 2, 2, 2, 12, 16, 35, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 26, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 821) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001143972526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143972526 none CC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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: [1, 1, 1, 1, 1, 2, 2, 2, 12, 16, 35, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 26, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972526 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972526 Building ZINC001143972575 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972575 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/822 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001143972575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972575 none CC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 17, 29, 29, 29, 29, 29, 10, 20, 20, 20, 1, 1, 1, 1, 1, 3, 17, 17, 29, 29, 29, 29, 29, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/823 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001143972575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972575 none CC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 24, 35, 35, 35, 35, 35, 12, 21, 21, 21, 1, 1, 1, 1, 1, 3, 24, 24, 35, 35, 35, 35, 35, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972575 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 Building ZINC001143972575 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972575 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 822) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001143972575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972575 none CC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 17, 29, 29, 29, 29, 29, 10, 20, 20, 20, 1, 1, 1, 1, 1, 3, 17, 17, 29, 29, 29, 29, 29, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 823) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001143972575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972575 none CC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 24, 35, 35, 35, 35, 35, 12, 21, 21, 21, 1, 1, 1, 1, 1, 3, 24, 24, 35, 35, 35, 35, 35, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972575 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972575 Building ZINC001143972576 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972576 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/824 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001143972576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972576 none CC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 24, 35, 35, 35, 35, 35, 12, 21, 21, 21, 1, 1, 1, 1, 1, 3, 24, 24, 35, 35, 35, 35, 35, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/825 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001143972576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972576 none CC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 17, 29, 29, 29, 29, 29, 10, 20, 20, 20, 1, 1, 1, 1, 1, 3, 17, 17, 29, 29, 29, 29, 29, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972576 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 Building ZINC001143972576 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972576 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 824) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001143972576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972576 none CC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 24, 35, 35, 35, 35, 35, 12, 21, 21, 21, 1, 1, 1, 1, 1, 3, 24, 24, 35, 35, 35, 35, 35, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 825) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001143972576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143972576 none CC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 17, 29, 29, 29, 29, 29, 10, 20, 20, 20, 1, 1, 1, 1, 1, 3, 17, 17, 29, 29, 29, 29, 29, 20, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972576 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972576 Building ZINC001143972888 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972888 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/826 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC) `ZINC001143972888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143972888 none CC[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 15, 23, 35, 35, 35, 35, 35, 7, 14, 14, 14, 1, 1, 1, 1, 1, 2, 17, 17, 22, 23, 35, 35, 35, 35, 35, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/827 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC) `ZINC001143972888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143972888 none CC[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 16, 24, 34, 34, 34, 34, 34, 7, 14, 14, 14, 1, 1, 1, 1, 1, 2, 18, 18, 22, 24, 34, 34, 34, 34, 34, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972888 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 Building ZINC001143972888 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972888 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 826) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC) `ZINC001143972888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143972888 none CC[C@@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 15, 23, 35, 35, 35, 35, 35, 7, 14, 14, 14, 1, 1, 1, 1, 1, 2, 17, 17, 22, 23, 35, 35, 35, 35, 35, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 827) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC) `ZINC001143972888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001143972888 none CC[C@]([O-])([SiH3])C(=O)N[C@@H](CCc1cn(C)cn1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 1, 1, 8, 5, 1, 8, 1, 11, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 16, 24, 34, 34, 34, 34, 34, 7, 14, 14, 14, 1, 1, 1, 1, 1, 2, 18, 18, 22, 24, 34, 34, 34, 34, 34, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143972888 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143972888 Building ZINC001143973011 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143973011 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/828 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001143973011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143973011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143973011 none CC[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 21, 37, 37, 37, 37, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 3, 14, 14, 37, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/829 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001143973011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143973011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143973011 none CC[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 21, 36, 36, 36, 36, 50, 50, 50, 36, 36, 1, 1, 1, 1, 1, 2, 14, 14, 36, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143973011 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 Building ZINC001143973011 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143973011 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 828) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001143973011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143973011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143973011 none CC[C@@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 21, 37, 37, 37, 37, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 3, 14, 14, 37, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 829) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1) `ZINC001143973011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143973011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001143973011 none CC[C@]([O-])([SiH3])C(=O)NCC1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 21, 36, 36, 36, 36, 50, 50, 50, 36, 36, 1, 1, 1, 1, 1, 2, 14, 14, 36, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 36] 50 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143973011 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973011 Building ZINC001143973083 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143973083 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/830 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001143973083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143973083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143973083 none CC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 30, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 41, 41, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/831 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001143973083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143973083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143973083 none CC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 29, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 41, 41, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143973083 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 Building ZINC001143973083 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143973083 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 830) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001143973083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143973083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143973083 none CC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 30, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 41, 41, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 831) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001143973083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143973083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001143973083 none CC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 29, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 41, 41, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143973083 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143973083 Building ZINC001143979888 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143979888 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/832 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])CC) `ZINC001143979888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143979888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143979888 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 29, 11, 29, 3, 11, 11, 20, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 1, 41, 41, 41, 41, 41, 20, 20, 24, 24, 3, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/833 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])CC) `ZINC001143979888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143979888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143979888 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 28, 25, 11, 25, 3, 11, 11, 19, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 1, 38, 38, 38, 38, 38, 19, 19, 24, 24, 3, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143979888 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 Building ZINC001143979888 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143979888 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 832) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])CC) `ZINC001143979888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143979888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143979888 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 31, 29, 11, 29, 3, 11, 11, 20, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 1, 41, 41, 41, 41, 41, 20, 20, 24, 24, 3, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 833) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])CC) `ZINC001143979888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143979888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001143979888 none CCOC(=O)[C@H](Cc1cnc[nH]1)NC(=O)[C@@]([O-])([SiH3])CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 8, 1, 8, 6, 8, 1, 11, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 28, 25, 11, 25, 3, 11, 11, 19, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 1, 38, 38, 38, 38, 38, 19, 19, 24, 24, 3, 1, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001143979888 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001143979888 Building ZINC001144029506 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144029506 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/834 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1) `ZINC001144029506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144029506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144029506 none CCC[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 17, 17, 38, 38, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/835 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1) `ZINC001144029506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144029506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144029506 none CCC[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 15, 38, 38, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144029506 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 Building ZINC001144029506 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144029506 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 834) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1) `ZINC001144029506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144029506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144029506 none CCC[C@@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 17, 17, 38, 38, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 3, 17, 17, 17, 17, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 145 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 835) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1) `ZINC001144029506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144029506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144029506 none CCC[C@]([O-])([SiH3])C(=O)NCCC(=O)N1CCOCC1 NO_LONG_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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 15, 38, 38, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 15, 15, 44, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144029506 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144029506 Building ZINC001144033162 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033162 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/836 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1) `ZINC001144033162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144033162 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 9, 18, 26, 26, 26, 26, 33, 33, 33, 26, 26, 7, 7, 7, 7, 7, 6, 6, 26, 26, 26, 26, 33, 33, 33, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/837 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1) `ZINC001144033162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144033162 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 8, 17, 27, 27, 27, 27, 32, 32, 32, 27, 27, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 32, 32, 32, 27, 27, 27, 27] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033162 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 Building ZINC001144033162 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033162 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 836) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1) `ZINC001144033162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144033162 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 9, 18, 26, 26, 26, 26, 33, 33, 33, 26, 26, 7, 7, 7, 7, 7, 6, 6, 26, 26, 26, 26, 33, 33, 33, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 837) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1) `ZINC001144033162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144033162 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 14, 5, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 8, 17, 27, 27, 27, 27, 32, 32, 32, 27, 27, 5, 5, 5, 5, 5, 5, 5, 27, 27, 27, 27, 32, 32, 32, 27, 27, 27, 27] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033162 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033162 Building ZINC001144033488 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144033488 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/838 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/839 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/840 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/840' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/841 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/841' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033488 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 Building ZINC001144033488 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144033488 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 838) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 839) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 840) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 841) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033488 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 Building ZINC001144033488 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144033488 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 838) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 839) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 840) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 841) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033488 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 Building ZINC001144033488 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144033488 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 838) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 839) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 840) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 16, 16, 23, 39, 39, 39, 39, 39, 39, 39, 16, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 39, 39, 39, 39, 39, 39, 39, 39, 39, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 87 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 841) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1) `ZINC001144033488.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144033488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033488 none CCC[C@]([O-])([SiH3])C(=O)N1CC(N2CCN(C)C(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 5, 1, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 4, 6, 15, 15, 23, 33, 33, 33, 33, 33, 33, 33, 15, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033488 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033488 Building ZINC001144033492 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033492 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/842 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001144033492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033492 none CCC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 25, 37, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 37, 37, 37, 37, 5, 5] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/843 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001144033492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033492 none CCC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 34, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 18, 18, 34, 34, 34, 34, 4, 4] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033492 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 Building ZINC001144033492 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033492 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 842) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001144033492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033492 none CCC[C@@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 25, 37, 37, 37, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 37, 37, 37, 37, 5, 5] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 843) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1) `ZINC001144033492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033492 none CCC[C@]([O-])([SiH3])C(=O)N1CCn2c(CNC(C)=O)nnc2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 8, 1, 5, 11, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 18, 34, 34, 34, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 18, 18, 34, 34, 34, 34, 4, 4] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033492 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033492 Building ZINC001144033767 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033767 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/844 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1) `ZINC001144033767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144033767 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 6, 10, 10, 10, 10, 25, 39, 39, 39, 10, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 25, 25, 39, 39, 39, 10, 10, 10, 10] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/845 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1) `ZINC001144033767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144033767 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 14, 34, 34, 34, 6, 6, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 14, 14, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033767 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 Building ZINC001144033767 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033767 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 844) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1) `ZINC001144033767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144033767 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 6, 10, 10, 10, 10, 25, 39, 39, 39, 10, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 25, 25, 39, 39, 39, 10, 10, 10, 10] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 845) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1) `ZINC001144033767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144033767 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(CC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 11, 12, 5, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 14, 34, 34, 34, 6, 6, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 14, 14, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033767 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033767 Building ZINC001144033768 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033768 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/846 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033768 none CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/847 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033768 none CCC[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033768 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 Building ZINC001144033768 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033768 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 846) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033768.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033768 none CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 847) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033768.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033768 none CCC[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 4, 15, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033768 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033768 Building ZINC001144033769 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033769 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/848 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033769 none CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 4, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/849 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033769 none CCC[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 4, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 34, 34, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 34, 34, 34] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033769 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 Building ZINC001144033769 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033769 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 848) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033769 none CCC[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 4, 21, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 6, 6, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 849) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O) `ZINC001144033769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001144033769 none CCC[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CNC(=O)CN2C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 4, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 34, 34, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 34, 34, 34] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 75 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033769 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033769 Building ZINC001144033830 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033830 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/850 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001144033830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144033830 none CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 2, 9, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/851 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001144033830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144033830 none CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 8, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033830 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 Building ZINC001144033830 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033830 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 850) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001144033830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144033830 none CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 2, 9, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 851) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2) `ZINC001144033830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144033830 none CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)CNC(=O)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 2, 8, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5, 5, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033830 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033830 Building ZINC001144033957 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033957 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/852 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC) `ZINC001144033957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033957 none CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 16, 16, 33, 33, 33, 33, 33] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/853 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC) `ZINC001144033957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033957 none CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 33, 33, 33, 34, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 18, 18, 34, 34, 34, 34, 34] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033957 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 Building ZINC001144033957 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033957 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 852) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC) `ZINC001144033957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033957 none CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 33, 33, 33, 33, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 16, 16, 33, 33, 33, 33, 33] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 853) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC) `ZINC001144033957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033957 none CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 33, 33, 33, 34, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 18, 18, 34, 34, 34, 34, 34] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033957 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033957 Building ZINC001144033959 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033959 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/854 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC) `ZINC001144033959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033959 none CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 33, 33, 33, 34, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 17, 17, 34, 34, 34, 34, 34] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/855 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC) `ZINC001144033959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033959 none CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 15, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 15, 15, 32, 32, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033959 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 Building ZINC001144033959 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033959 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 854) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC) `ZINC001144033959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033959 none CCC[C@@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 33, 33, 33, 34, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 17, 17, 34, 34, 34, 34, 34] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 855) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC) `ZINC001144033959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144033959 none CCC[C@]([O-])([SiH3])C(=O)N1CCNC(=O)[C@@H]1CC(=O)OCC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 5, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 2, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 15, 32, 32, 32, 32, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 15, 15, 32, 32, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 112 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033959 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033959 Building ZINC001144033990 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033990 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/856 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1) `ZINC001144033990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033990 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 2, 18, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/857 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1) `ZINC001144033990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033990 none CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 1, 1, 1, 2, 19, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033990 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 Building ZINC001144033990 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033990 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 856) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1) `ZINC001144033990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033990 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 2, 18, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 78 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 857) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1) `ZINC001144033990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033990 none CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 1, 1, 1, 2, 19, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 9, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 82 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033990 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033990 Building ZINC001144033991 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033991 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/858 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1) `ZINC001144033991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033991 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 1, 1, 1, 2, 16, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/859 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1) `ZINC001144033991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033991 none CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 2, 16, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033991 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 Building ZINC001144033991 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144033991 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 858) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1) `ZINC001144033991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144033991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033991 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 1, 1, 1, 2, 16, 20, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 859) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1) `ZINC001144033991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144033991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144033991 none CCC[C@]([O-])([SiH3])C(=O)N1CCN2C(=O)COC[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 2, 16, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144033991 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144033991 Building ZINC001144034070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/860 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/861 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/862 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/862' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/863 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/863' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 Building ZINC001144034070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 860) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 861) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 862) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 863) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 Building ZINC001144034070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 860) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 861) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 862) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 863) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 Building ZINC001144034070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 860) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 861) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 862) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 9, 16, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 32, 32, 32, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 863) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1) `ZINC001144034070.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034070 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 8, 14, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 7, 7, 7, 7, 7, 6, 6, 16, 16, 16, 16, 16, 16, 16, 28, 28, 28, 16, 16] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034070 Building ZINC001144034073 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034073 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/864 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/865 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/866 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/866' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/867 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/867' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034073 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 Building ZINC001144034073 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034073 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 864) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 865) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 866) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 867) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034073 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 Building ZINC001144034073 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034073 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 864) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 865) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 866) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 867) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034073 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 Building ZINC001144034073 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144034073 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 864) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 865) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 866) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 9, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 11, 11] 33 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 867) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1) `ZINC001144034073.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144034073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144034073 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 8, 8] 24 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034073 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034073 Building ZINC001144034557 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144034557 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/868 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)C1) `ZINC001144034557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001144034557 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 31, 31, 15, 15, 15, 8, 8, 8, 8, 8, 7, 7, 15, 15, 31, 31, 31, 31, 31, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/869 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)C1) `ZINC001144034557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001144034557 none CCC[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 30, 30, 12, 12, 12, 8, 8, 8, 8, 8, 7, 7, 12, 12, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034557 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 Building ZINC001144034557 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144034557 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 868) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)C1) `ZINC001144034557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144034557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001144034557 none CCC[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 31, 31, 15, 15, 15, 8, 8, 8, 8, 8, 7, 7, 15, 15, 31, 31, 31, 31, 31, 15, 15] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 869) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)C1) `ZINC001144034557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144034557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001144034557 none CCC[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C2CC2)C(=O)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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 30, 30, 12, 12, 12, 8, 8, 8, 8, 8, 7, 7, 12, 12, 30, 30, 30, 30, 30, 12, 12] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144034557 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144034557 Building ZINC001144035225 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144035225 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/870 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001144035225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144035225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144035225 none CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 7, 24, 35, 35, 35, 35, 30, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 34, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/871 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001144035225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144035225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144035225 none CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 8, 21, 32, 32, 32, 32, 27, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 31, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144035225 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 Building ZINC001144035225 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144035225 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 870) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001144035225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144035225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144035225 none CCC[C@@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 7, 24, 35, 35, 35, 35, 30, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 34, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 871) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2) `ZINC001144035225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144035225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144035225 none CCC[C@]([O-])([SiH3])C(=O)N1CCC2(CC1)COCC(=O)N2 NO_LONG_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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 8, 21, 32, 32, 32, 32, 27, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 31, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144035225 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144035225 Building ZINC001144037167 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144037167 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/872 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1) `ZINC001144037167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144037167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144037167 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 2, 11, 17, 21, 21, 21, 21, 30, 30, 21, 30, 30, 21, 21, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 30, 30, 21, 21, 21, 21] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/873 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1) `ZINC001144037167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144037167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144037167 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 2, 10, 18, 23, 23, 23, 23, 30, 30, 23, 30, 30, 23, 23, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 30, 30, 23, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144037167 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 Building ZINC001144037167 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144037167 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 872) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1) `ZINC001144037167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144037167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144037167 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 2, 11, 17, 21, 21, 21, 21, 30, 30, 21, 30, 30, 21, 21, 7, 7, 7, 7, 7, 7, 7, 21, 21, 21, 21, 30, 30, 21, 21, 21, 21] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 873) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1) `ZINC001144037167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144037167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001144037167 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(c2ncncn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 8, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 2, 10, 18, 23, 23, 23, 23, 30, 30, 23, 30, 30, 23, 23, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 30, 30, 23, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 96 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144037167 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144037167 Building ZINC001144038230 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038230 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/874 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/875 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/876 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/876' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/877 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/877' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038230 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 Building ZINC001144038230 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038230 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 874) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 875) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 876) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 877) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038230 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 Building ZINC001144038230 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038230 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 874) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 875) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 876) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 877) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038230 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 Building ZINC001144038230 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038230 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 874) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 875) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 876) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 32, 32, 32] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 103 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 877) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC) `ZINC001144038230.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038230 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 10, 12, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 29, 29, 29] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038230 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038230 Building ZINC001144038231 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038231 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/878 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/879 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/880 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/880' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/881 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/881' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038231 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 Building ZINC001144038231 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038231 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 878) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 879) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 880) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 881) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038231 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 Building ZINC001144038231 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038231 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 878) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 879) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 880) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 881) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038231 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 Building ZINC001144038231 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001144038231 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 878) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 879) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 880) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23, 7, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 23, 23, 23] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 881) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC) `ZINC001144038231.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001144038231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144038231 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C)C[C@H]1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 7, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 9, 11, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 31] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038231 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038231 Building ZINC001144038327 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144038327 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/882 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001144038327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038327 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 17, 17, 12, 12, 12, 24, 24, 24, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 17, 17, 17, 24, 24, 24, 12, 12] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/883 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001144038327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038327 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 11, 11, 12, 12, 12, 12, 20, 20, 12, 12, 12, 22, 22, 22, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 20, 20, 20, 22, 22, 22, 12, 12] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038327 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 Building ZINC001144038327 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144038327 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 882) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001144038327.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038327 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 9, 9, 12, 12, 12, 12, 17, 17, 12, 12, 12, 24, 24, 24, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 17, 17, 17, 24, 24, 24, 12, 12] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 883) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1) `ZINC001144038327.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038327 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 2, 11, 11, 12, 12, 12, 12, 20, 20, 12, 12, 12, 22, 22, 22, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 20, 20, 20, 22, 22, 22, 12, 12] 50 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038327 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038327 Building ZINC001144038329 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144038329 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/884 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001144038329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038329 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 5, 5, 5, 3, 7, 7, 7, 7, 7, 6, 6, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3] 17 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/885 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001144038329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038329 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 8, 8, 6, 6, 6, 10, 10, 10, 6, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 8, 8, 8, 10, 10, 10, 6, 6] 21 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038329 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 Building ZINC001144038329 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144038329 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 884) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001144038329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144038329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038329 none CCC[C@@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 5, 5, 5, 3, 7, 7, 7, 7, 7, 6, 6, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 3, 3] 17 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 885) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1) `ZINC001144038329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144038329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001144038329 none CCC[C@]([O-])([SiH3])C(=O)N1CCN(C(C)=O)[C@@H](C(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 1, 11, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 2, 4, 4, 6, 6, 6, 6, 8, 8, 6, 6, 6, 10, 10, 10, 6, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 8, 8, 8, 10, 10, 10, 6, 6] 21 rigid atoms, others: [2, 3, 4] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144038329 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144038329 Building ZINC001144043545 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144043545 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/886 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001144043545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001144043545 none CCC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 5, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 11, 19, 47, 47, 47] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/887 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001144043545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001144043545 none CCC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 5, 5, 12, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 12, 19, 44, 44, 44] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144043545 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 Building ZINC001144043545 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144043545 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 886) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001144043545.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001144043545 none CCC[C@@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 5, 5, 11, 19, 19, 19, 19, 19, 19, 19, 19, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 11, 19, 47, 47, 47] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 887) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC) `ZINC001144043545.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144043545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001144043545 none CCC[C@]([O-])([SiH3])C(=O)Nc1[nH]c(=O)cnc1C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 6, 1, 11, 1, 8, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 4, 7, 7, 6, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 5, 5, 12, 19, 19, 19, 19, 19, 19, 19, 19, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 12, 19, 44, 44, 44] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144043545 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144043545 Building ZINC001144044032 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144044032 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/888 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O) `ZINC001144044032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144044032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044032 none CCC[C@@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 18, 9, 9, 9, 9, 17, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/889 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O) `ZINC001144044032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144044032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044032 none CCC[C@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 18, 9, 9, 9, 9, 17, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144044032 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 Building ZINC001144044032 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144044032 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 888) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O) `ZINC001144044032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144044032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044032 none CCC[C@@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 18, 9, 9, 9, 9, 17, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 889) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O) `ZINC001144044032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144044032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044032 none CCC[C@]([O-])([SiH3])C(=O)Nc1c(N)n(CC)c(=O)n(CC)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 18, 9, 9, 9, 9, 17, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144044032 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044032 Building ZINC001144044758 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144044758 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/890 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O) `ZINC001144044758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144044758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144044758 none CCC[C@@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 36, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 25, 25, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/891 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O) `ZINC001144044758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144044758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144044758 none CCC[C@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 36, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 25, 25, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144044758 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 Building ZINC001144044758 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144044758 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 890) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O) `ZINC001144044758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144044758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144044758 none CCC[C@@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 36, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 25, 25, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 891) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O) `ZINC001144044758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144044758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001144044758 none CCC[C@]([O-])([SiH3])C(=O)NCCN1CCCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 36, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 25, 25, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144044758 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044758 Building ZINC001144044873 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144044873 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/892 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001144044873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144044873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044873 none CCC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 27, 26, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/893 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001144044873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144044873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044873 none CCC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 26, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144044873 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 Building ZINC001144044873 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144044873 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 892) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001144044873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144044873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044873 none CCC[C@@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 27, 26, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 893) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1) `ZINC001144044873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144044873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001144044873 none CCC[C@]([O-])([SiH3])C(=O)NCCCN1CCS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 26, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144044873 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144044873 Building ZINC001144045029 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045029 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/894 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001144045029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045029 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 22, 28, 28, 28, 28, 28, 13, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 3, 22, 22, 28, 28, 28, 28, 28, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/895 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001144045029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045029 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 27, 27, 27, 27, 27, 11, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 27, 27, 27, 27, 27, 22, 22, 22] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144045029 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 Building ZINC001144045029 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045029 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 894) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001144045029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045029 none CCC[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 22, 28, 28, 28, 28, 28, 13, 26, 26, 26, 4, 4, 4, 4, 4, 4, 4, 3, 22, 22, 28, 28, 28, 28, 28, 26, 26, 26] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 895) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC) `ZINC001144045029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045029 none CCC[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 20, 27, 27, 27, 27, 27, 11, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 3, 20, 20, 27, 27, 27, 27, 27, 22, 22, 22] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144045029 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045029 Building ZINC001144045030 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045030 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/896 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001144045030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045030 none CCC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 19, 26, 26, 26, 26, 26, 11, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 3, 19, 19, 26, 26, 26, 26, 26, 22, 22, 22] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/897 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/897' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001144045030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045030 none CCC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 21, 27, 27, 27, 27, 27, 13, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 27, 27, 27, 27, 27, 24, 24, 24] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144045030 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 Building ZINC001144045030 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045030 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 896) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001144045030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045030 none CCC[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 11, 11, 19, 26, 26, 26, 26, 26, 11, 22, 22, 22, 4, 4, 4, 4, 4, 4, 4, 3, 19, 19, 26, 26, 26, 26, 26, 22, 22, 22] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 897) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC) `ZINC001144045030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001144045030 none CCC[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cncn1C)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 8, 1, 8, 5, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 13, 21, 27, 27, 27, 27, 27, 13, 24, 24, 24, 4, 4, 4, 4, 4, 4, 4, 3, 21, 21, 27, 27, 27, 27, 27, 24, 24, 24] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144045030 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045030 Building ZINC001144045815 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045815 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/898 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001144045815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144045815 none CCC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 16, 29, 44, 46, 45, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 16, 16, 44, 44, 46, 46, 46, 46] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/899 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001144045815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144045815 none CCC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 16, 29, 44, 46, 45, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 16, 16, 44, 44, 46, 46, 46, 46] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144045815 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 Building ZINC001144045815 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144045815 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 898) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001144045815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144045815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144045815 none CCC[C@@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 16, 29, 44, 46, 45, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 16, 16, 44, 44, 46, 46, 46, 46] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 899) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O) `ZINC001144045815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144045815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001144045815 none CCC[C@]([O-])([SiH3])C(=O)NCCOCCN1C(=O)C=CC1=O NO_LONG_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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 8, 1, 11, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 3, 3, 3, 15, 16, 29, 44, 46, 45, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 5, 3, 15, 15, 16, 16, 44, 44, 46, 46, 46, 46] 50 rigid atoms, others: [2, 3, 4, 5] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001144045815 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001144045815 Building ZINC001148876645 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001148876645 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/900 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001148876645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001148876645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001148876645 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 34, 11, 11, 11, 31, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 34, 34, 102, 31, 31, 93, 11, 11] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 401 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/901 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001148876645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001148876645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001148876645 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 31, 11, 11, 11, 30, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 31, 31, 93, 30, 30, 90, 11, 11] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001148876645 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 Building ZINC001148876645 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001148876645 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 900) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001148876645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001148876645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001148876645 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 34, 11, 11, 11, 31, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 34, 34, 102, 31, 31, 93, 11, 11] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 401 number of broken/clashed sets: 76 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 901) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC001148876645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001148876645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001148876645 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 31, 11, 11, 11, 30, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 31, 31, 93, 30, 30, 90, 11, 11] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001148876645 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001148876645 Building ZINC001149431663 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431663 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/902 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/903 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/904 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/904' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/905 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/905' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431663 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 Building ZINC001149431663 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431663 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 902) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 903) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 904) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 905) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431663 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 Building ZINC001149431663 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431663 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 902) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 903) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 904) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 905) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431663 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 Building ZINC001149431663 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431663 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 902) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 903) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 904) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 37, 37, 37, 37, 50, 50, 50, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 37, 37, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 905) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1) `ZINC001149431663.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431663 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431663 Building ZINC001149431664 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431664 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/906 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/907 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/908 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/908' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/909 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/909' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431664 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 Building ZINC001149431664 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431664 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 906) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 907) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 908) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 909) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431664 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 Building ZINC001149431664 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431664 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 906) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 907) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 908) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 909) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431664 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 Building ZINC001149431664 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149431664 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 906) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 907) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 908) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 38, 38, 38, 38, 50, 50, 50, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 38, 38, 50, 50, 50, 50, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 909) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1) `ZINC001149431664.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149431664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149431664 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CC(N)=O)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 1, 8, 11, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 39, 39, 50, 50, 50, 50, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149431664 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149431664 Building ZINC001149439111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/910 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/911 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/912 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/912' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/913 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/913' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 Building ZINC001149439111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 910) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 911) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 912) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 913) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 Building ZINC001149439111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 910) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 911) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 912) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 913) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 Building ZINC001149439111 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439111 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 910) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 911) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 912) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 46, 46, 46, 46, 50, 50, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 46, 46, 50, 50, 50, 50, 150, 46, 46, 46, 46, 46, 46] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 913) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1) `ZINC001149439111.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439111 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439111 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439111 Building ZINC001149439112 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439112 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/914 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/915 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/916 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/916' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/917 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/917' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439112 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 Building ZINC001149439112 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439112 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 914) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 915) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 916) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 917) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439112 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 Building ZINC001149439112 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439112 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 914) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 915) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 916) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 917) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439112 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 Building ZINC001149439112 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001149439112 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 914) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 915) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `2' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 2 (index: 916) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 47, 47, 47, 47, 50, 50, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 47, 47, 50, 50, 50, 50, 150, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `3' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 3 (index: 917) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1) `ZINC001149439112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001149439112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001149439112 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CN(CCO)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 42, 42, 42, 42, 50, 50, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 42, 42, 50, 50, 50, 50, 150, 42, 42, 42, 42, 42, 42] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 312 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001149439112 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 3: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/3.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/0.* 2: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112/2.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001149439112 Building ZINC001150087302 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150087302 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/918 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1) `ZINC001150087302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150087302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150087302 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 8, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 7, 7, 7, 22, 27, 27, 27, 7, 4, 4, 4, 4, 2, 4, 4, 7, 7, 7, 22, 27, 27, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/919 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1) `ZINC001150087302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150087302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150087302 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 8, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 7, 7, 7, 21, 31, 31, 31, 7, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 21, 31, 31, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150087302 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 Building ZINC001150087302 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150087302 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 918) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1) `ZINC001150087302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150087302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150087302 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 8, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 7, 7, 7, 22, 27, 27, 27, 7, 4, 4, 4, 4, 2, 4, 4, 7, 7, 7, 22, 27, 27, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 919) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1) `ZINC001150087302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150087302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150087302 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(NS(N)(=O)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 14, 8, 11, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 7, 7, 7, 21, 31, 31, 31, 7, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 21, 31, 31, 7, 7, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150087302 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150087302 Building ZINC001150119033 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150119033 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/920 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1) `ZINC001150119033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150119033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001150119033 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 5, 16, 16, 16, 16, 29, 29, 16, 6, 6, 6, 6, 2, 6, 6, 16, 16, 48, 29, 29, 16, 16, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/921 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1) `ZINC001150119033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150119033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001150119033 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 5, 16, 16, 16, 16, 32, 32, 16, 4, 4, 4, 4, 2, 4, 4, 16, 16, 48, 32, 32, 16, 16, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150119033 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 Building ZINC001150119033 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150119033 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 920) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1) `ZINC001150119033.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150119033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001150119033 none Cc1cccc([C@@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 2, 6, 6, 1, 1, 1, 1, 3, 5, 16, 16, 16, 16, 29, 29, 16, 6, 6, 6, 6, 2, 6, 6, 16, 16, 48, 29, 29, 16, 16, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 921) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1) `ZINC001150119033.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150119033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001150119033 none Cc1cccc([C@]([O-])([SiH3])C(=O)N2CC(O)(C(N)=O)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 11, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 2, 4, 4, 1, 1, 1, 1, 3, 5, 16, 16, 16, 16, 32, 32, 16, 4, 4, 4, 4, 2, 4, 4, 16, 16, 48, 32, 32, 16, 16, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150119033 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150119033 Building ZINC001150804465 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150804465 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/922 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1) `ZINC001150804465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150804465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804465 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 2, 18, 19, 26, 26, 26, 26, 26, 26, 26, 41, 41, 41, 41, 41, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/923 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1) `ZINC001150804465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150804465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804465 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 2, 18, 20, 27, 27, 27, 27, 27, 27, 27, 39, 39, 39, 39, 39, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150804465 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 Building ZINC001150804465 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150804465 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 922) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1) `ZINC001150804465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150804465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804465 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 2, 18, 19, 26, 26, 26, 26, 26, 26, 26, 41, 41, 41, 41, 41, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 923) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1) `ZINC001150804465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150804465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804465 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 2, 18, 20, 27, 27, 27, 27, 27, 27, 27, 39, 39, 39, 39, 39, 7, 7, 7, 7, 7, 7, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150804465 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804465 Building ZINC001150804466 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150804466 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/924 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1) `ZINC001150804466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150804466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804466 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 16, 16, 23, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/925 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1) `ZINC001150804466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150804466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804466 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 20, 21, 26, 26, 26, 26, 26, 26, 26, 42, 42, 42, 42, 42, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150804466 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 Building ZINC001150804466 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001150804466 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 924) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1) `ZINC001150804466.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001150804466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804466 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 16, 16, 23, 23, 23, 23, 23, 23, 23, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 925) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1) `ZINC001150804466.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001150804466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001150804466 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 8, 8, 8, 6, 8, 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, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 20, 21, 26, 26, 26, 26, 26, 26, 26, 42, 42, 42, 42, 42, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26] 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]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001150804466 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001150804466 Building ZINC001151838803 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151838803 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/926 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1) `ZINC001151838803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151838803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001151838803 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 7, 7, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 23, 23, 23, 23, 23, 7, 13, 13, 13, 13, 39, 39, 13, 13, 7] 450 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/927 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1) `ZINC001151838803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151838803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001151838803 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 14, 14, 14, 14, 14, 5, 15, 15, 15, 15, 45, 45, 15, 15, 5] 450 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001151838803 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 Building ZINC001151838803 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001151838803 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 926) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1) `ZINC001151838803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001151838803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001151838803 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 7, 7, 1, 1, 1, 2, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 23, 23, 23, 23, 23, 7, 13, 13, 13, 13, 39, 39, 13, 13, 7] 450 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 927) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1) `ZINC001151838803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001151838803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001151838803 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](O)[C@@H](O)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 7, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 2, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 14, 14, 14, 14, 14, 5, 15, 15, 15, 15, 45, 45, 15, 15, 5] 450 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001151838803 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001151838803 Building ZINC001152311954 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152311954 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/928 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1) `ZINC001152311954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152311954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001152311954 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 4, 4, 15, 15, 15, 15, 15, 4, 8, 8, 24, 8, 8, 17, 17, 17, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/929 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1) `ZINC001152311954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152311954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001152311954 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 4, 4, 10, 10, 10, 10, 10, 4, 8, 8, 24, 8, 8, 15, 15, 15, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152311954 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 Building ZINC001152311954 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152311954 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 928) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1) `ZINC001152311954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152311954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001152311954 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 4, 4, 4, 1, 1, 1, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 4, 4, 15, 15, 15, 15, 15, 4, 8, 8, 24, 8, 8, 17, 17, 17, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 929) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1) `ZINC001152311954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152311954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001152311954 none CCn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2C(=O)OC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 4, 4, 10, 10, 10, 10, 10, 4, 8, 8, 24, 8, 8, 15, 15, 15, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152311954 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152311954 Building ZINC001152442405 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152442405 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/930 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1C) `ZINC001152442405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152442405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001152442405 none Cc1nnc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 16, 16, 4, 10, 10, 10, 10, 10, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/931 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1C) `ZINC001152442405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152442405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001152442405 none Cc1nnc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 17, 17, 4, 10, 10, 10, 10, 10, 25, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152442405 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 Building ZINC001152442405 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152442405 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 930) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1C) `ZINC001152442405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152442405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001152442405 none Cc1nnc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 16, 16, 4, 10, 10, 10, 10, 10, 23, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 931) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1C) `ZINC001152442405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152442405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001152442405 none Cc1nnc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 25, 25, 25, 25, 25, 17, 17, 4, 10, 10, 10, 10, 10, 25, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152442405 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152442405 Building ZINC001152486332 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152486332 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/932 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1) `ZINC001152486332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152486332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152486332 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 8, 6, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 2, 7, 11, 15, 15, 15, 15, 39, 39, 39, 39, 39, 15, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/933 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1) `ZINC001152486332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152486332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152486332 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 8, 6, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 6, 11, 14, 14, 14, 14, 34, 34, 34, 34, 34, 14, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152486332 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 Building ZINC001152486332 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152486332 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 932) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1) `ZINC001152486332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152486332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152486332 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 8, 6, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 2, 7, 11, 15, 15, 15, 15, 39, 39, 39, 39, 39, 15, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 933) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1) `ZINC001152486332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152486332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152486332 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(c3nn[nH]n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 8, 8, 6, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 6, 11, 14, 14, 14, 14, 34, 34, 34, 34, 34, 14, 14, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152486332 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152486332 Building ZINC001152489793 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152489793 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/934 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1) `ZINC001152489793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152489793 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 16, 16, 32, 16, 32, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 32, 32, 96, 32, 32, 39, 39] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 330 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/935 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1) `ZINC001152489793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152489793 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 15, 15, 36, 15, 30, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 36, 36, 108, 30, 30, 35, 35] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 341 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152489793 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 Building ZINC001152489793 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001152489793 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 934) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1) `ZINC001152489793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001152489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152489793 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 16, 16, 32, 16, 32, 39, 39, 39, 39, 39, 5, 5, 5, 5, 5, 5, 5, 32, 32, 96, 32, 32, 39, 39] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 330 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 935) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1) `ZINC001152489793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001152489793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001152489793 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)Cc1cnc[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 8, 1, 8, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 15, 15, 36, 15, 30, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 36, 36, 108, 30, 30, 35, 35] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 341 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001152489793 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001152489793 Building ZINC001153552530 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153552530 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/936 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1) `ZINC001153552530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153552530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001153552530 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/937 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1) `ZINC001153552530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153552530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001153552530 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153552530 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 Building ZINC001153552530 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153552530 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 936) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1) `ZINC001153552530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153552530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001153552530 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 937) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1) `ZINC001153552530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153552530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001153552530 none Cn1cc([C@]([O-])([SiH3])C(=O)NCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 16, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6, 6, 6, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153552530 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153552530 Building ZINC001153849398 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153849398 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/938 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153849398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849398 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 6, 23, 23, 23, 23, 23, 23, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/939 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153849398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849398 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 5, 27, 27, 27, 27, 27, 27, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153849398 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 Building ZINC001153849398 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153849398 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 938) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153849398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849398 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 6, 23, 23, 23, 23, 23, 23, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 939) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153849398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849398 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 1, 1, 1, 1, 5, 5, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 5, 27, 27, 27, 27, 27, 27, 12] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153849398 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849398 Building ZINC001153849399 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153849399 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/940 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153849399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849399 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 5, 26, 26, 26, 26, 26, 26, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/941 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153849399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849399 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 24, 24, 24, 24, 24, 24, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153849399 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 Building ZINC001153849399 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153849399 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 940) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153849399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849399 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 5, 5, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 5, 26, 26, 26, 26, 26, 26, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 941) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1) `ZINC001153849399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153849399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001153849399 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3cccnc3NC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 8, 1, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 6, 24, 24, 24, 24, 24, 24, 11] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153849399 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153849399 Building ZINC001153962095 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153962095 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/942 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cn(C)nn1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001153962095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153962095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001153962095 none C[C@H](Cc1cn(C)nn1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 5, 8, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 14, 28, 32, 32, 32, 32, 32, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 28, 28, 32, 32, 32, 32, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/943 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cn(C)nn1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001153962095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153962095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001153962095 none C[C@H](Cc1cn(C)nn1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 5, 8, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 13, 13, 28, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 13, 28, 28, 32, 32, 32, 32, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153962095 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 Building ZINC001153962095 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001153962095 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 942) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cn(C)nn1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001153962095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001153962095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001153962095 none C[C@H](Cc1cn(C)nn1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 5, 8, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 3, 14, 14, 28, 32, 32, 32, 32, 32, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 14, 14, 14, 28, 28, 32, 32, 32, 32, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 943) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cn(C)nn1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001153962095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001153962095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001153962095 none C[C@H](Cc1cn(C)nn1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 5, 8, 8, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 4, 13, 13, 28, 32, 32, 32, 32, 32, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 13, 13, 13, 28, 28, 32, 32, 32, 32, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001153962095 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001153962095 Building ZINC001154203332 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154203332 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/944 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CONC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001154203332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154203332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001154203332 none CONC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 27, 10, 27, 10, 10, 10, 4, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 33, 33, 33, 29, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/945 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CONC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001154203332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154203332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001154203332 none CONC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 22, 8, 22, 8, 8, 8, 4, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 30, 30, 30, 25, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154203332 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 Building ZINC001154203332 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154203332 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 944) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CONC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001154203332.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154203332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001154203332 none CONC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 29, 27, 10, 27, 10, 10, 10, 4, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 33, 33, 33, 29, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 945) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CONC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC001154203332.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154203332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001154203332 none CONC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 25, 22, 8, 22, 8, 8, 8, 4, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 30, 30, 30, 25, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 8, 8, 8, 8] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154203332 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154203332 Building ZINC001154225950 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154225950 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/946 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1) `ZINC001154225950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154225950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001154225950 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 12, 8, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 48, 24, 24, 24, 7] 100 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/947 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1) `ZINC001154225950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154225950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001154225950 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 12, 8, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 48, 24, 24, 24, 7] 100 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154225950 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 Building ZINC001154225950 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154225950 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 946) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1) `ZINC001154225950.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154225950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001154225950 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 12, 8, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 48, 24, 24, 24, 7] 100 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 947) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1) `ZINC001154225950.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154225950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001154225950 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCc3c(O)ncnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 12, 8, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 11, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 7, 7, 7, 7, 7, 24, 24, 24, 24, 48, 24, 24, 24, 7] 100 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154225950 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154225950 Building ZINC001154481824 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154481824 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/948 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154481824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481824 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 22, 29, 29, 29, 29, 31, 31, 29, 29, 6, 6, 6, 6, 1, 6, 6, 4, 15, 15, 29, 29, 31, 31, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/949 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154481824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481824 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 29, 29, 29, 29, 30, 30, 29, 29, 6, 6, 6, 6, 1, 6, 6, 3, 14, 14, 29, 29, 30, 30, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154481824 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 Building ZINC001154481824 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154481824 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 948) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154481824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481824 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 4, 4, 4, 22, 29, 29, 29, 29, 31, 31, 29, 29, 6, 6, 6, 6, 1, 6, 6, 4, 15, 15, 29, 29, 31, 31, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 949) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154481824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481824 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 29, 29, 29, 29, 30, 30, 29, 29, 6, 6, 6, 6, 1, 6, 6, 3, 14, 14, 29, 29, 30, 30, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154481824 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481824 Building ZINC001154481825 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154481825 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/950 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154481825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481825 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 30, 30, 30, 30, 31, 31, 30, 30, 6, 6, 6, 6, 1, 6, 6, 3, 14, 14, 30, 30, 31, 31, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/951 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154481825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481825 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 22, 29, 29, 29, 29, 32, 32, 29, 29, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 29, 29, 32, 32, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154481825 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 Building ZINC001154481825 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154481825 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 950) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154481825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481825 none Cc1cccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 30, 30, 30, 30, 31, 31, 30, 30, 6, 6, 6, 6, 1, 6, 6, 3, 14, 14, 30, 30, 31, 31, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 951) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1) `ZINC001154481825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154481825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001154481825 none Cc1cccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CC(C(N)=O)=NO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.am', 'O.2', 'N.2', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 8, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 22, 29, 29, 29, 29, 32, 32, 29, 29, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 29, 29, 32, 32, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154481825 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154481825 Building ZINC001154576904 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154576904 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/952 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001154576904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154576904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001154576904 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 13, 28, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 13, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/953 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001154576904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154576904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001154576904 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 13, 28, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 13, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154576904 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 Building ZINC001154576904 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154576904 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 952) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001154576904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154576904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001154576904 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 13, 28, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 13, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 953) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001154576904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154576904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001154576904 none CN(C)C(=O)c1c[nH]nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 8, 6, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 28, 31, 13, 28, 13, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 13, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154576904 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154576904 Building ZINC001154804958 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154804958 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/954 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154804958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804958 none CNC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 15, 21, 9, 9, 9, 9, 9, 9, 4, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 9, 27, 27, 27, 27, 15, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/955 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154804958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804958 none CNC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 21, 26, 11, 11, 11, 11, 11, 11, 6, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 11, 30, 30, 30, 30, 21, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154804958 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 Building ZINC001154804958 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154804958 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 954) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154804958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804958 none CNC(=O)N[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 15, 21, 9, 9, 9, 9, 9, 9, 4, 2, 5, 1, 1, 1, 4, 4, 4, 4, 4, 9, 27, 27, 27, 27, 15, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 955) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154804958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804958 none CNC(=O)N[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 21, 26, 11, 11, 11, 11, 11, 11, 6, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 11, 30, 30, 30, 30, 21, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154804958 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804958 Building ZINC001154804959 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154804959 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/956 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154804959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804959 none CNC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 24, 26, 12, 12, 12, 12, 12, 12, 6, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 32, 32, 32, 32, 24, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 105 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/957 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154804959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804959 none CNC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 20, 23, 11, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 11, 29, 29, 29, 29, 20, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154804959 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 Building ZINC001154804959 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001154804959 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 956) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001154804959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804959 none CNC(=O)N[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 24, 26, 12, 12, 12, 12, 12, 12, 6, 2, 10, 1, 1, 1, 5, 5, 5, 5, 5, 12, 32, 32, 32, 32, 24, 12, 12, 12, 12, 12, 12, 5, 5, 5, 5, 5, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 105 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 957) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC001154804959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001154804959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001154804959 none CNC(=O)N[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 23, 20, 23, 11, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 11, 29, 29, 29, 29, 20, 11, 11, 11, 11, 11, 11, 4, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 94 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001154804959 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001154804959 Building ZINC001155733745 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155733745 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/958 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1) `ZINC001155733745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155733745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155733745 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 14, 14, 14, 14, 14, 14, 18, 18, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 42, 18, 18, 14, 14, 14, 14] 150 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/959 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1) `ZINC001155733745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155733745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155733745 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 6, 11, 12, 12, 12, 12, 12, 19, 19, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 36, 19, 19, 12, 12, 12, 12] 150 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155733745 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 Building ZINC001155733745 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155733745 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 958) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1) `ZINC001155733745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155733745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155733745 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 5, 14, 14, 14, 14, 14, 14, 18, 18, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 42, 18, 18, 14, 14, 14, 14] 150 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 88 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 959) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1) `ZINC001155733745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155733745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155733745 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCC(O)(C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 6, 11, 12, 12, 12, 12, 12, 19, 19, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 36, 19, 19, 12, 12, 12, 12] 150 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155733745 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155733745 Building ZINC001155898791 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155898791 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/960 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001155898791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155898791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155898791 none Cn1nnc(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 22, 16, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 38, 38, 22, 16, 16, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/961 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001155898791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155898791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155898791 none Cn1nnc(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 27, 16, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 40, 27, 16, 16, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155898791 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 Building ZINC001155898791 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155898791 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 960) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001155898791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155898791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155898791 none Cn1nnc(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 38, 22, 16, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 38, 38, 22, 16, 16, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 961) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnc(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001155898791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155898791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155898791 none Cn1nnc(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 40, 27, 16, 14, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 40, 40, 27, 16, 16, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155898791 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155898791 Building ZINC001155899076 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155899076 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/962 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001155899076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155899076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155899076 none Cn1nnnc1CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 32, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 32, 29, 24, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/963 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001155899076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155899076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155899076 none Cn1nnnc1CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 31, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 31, 29, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155899076 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 Building ZINC001155899076 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155899076 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 962) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001155899076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155899076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155899076 none Cn1nnnc1CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 32, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 32, 29, 24, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 963) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nnnc1CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001155899076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155899076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155899076 none Cn1nnnc1CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 31, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 31, 29, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155899076 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899076 Building ZINC001155899584 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155899584 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/964 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1) `ZINC001155899584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155899584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155899584 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 19, 32, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 19, 19, 32, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/965 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1) `ZINC001155899584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155899584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155899584 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 19, 33, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 14, 14, 17, 19, 33, 45, 45, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155899584 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 Building ZINC001155899584 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155899584 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 964) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1) `ZINC001155899584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155899584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155899584 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 19, 32, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 19, 19, 32, 40, 40, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 965) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1) `ZINC001155899584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155899584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155899584 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)N1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 19, 33, 45, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 14, 14, 17, 19, 33, 45, 45, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155899584 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899584 Building ZINC001155899790 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155899790 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/966 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1[nH]c(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1=O) `ZINC001155899790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155899790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155899790 none Cn1[nH]c(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.pl3', 'H', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 6, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 25, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 25, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/967 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1[nH]c(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1=O) `ZINC001155899790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155899790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155899790 none Cn1[nH]c(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.pl3', 'H', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 6, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 28, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 38, 26, 28, 18, 18, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155899790 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 Building ZINC001155899790 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155899790 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 966) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1[nH]c(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1=O) `ZINC001155899790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155899790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155899790 none Cn1[nH]c(CNCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.pl3', 'H', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 6, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 25, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 25, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 967) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1[nH]c(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1=O) `ZINC001155899790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155899790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155899790 none Cn1[nH]c(CNCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.pl3', 'H', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 6, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 28, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 38, 26, 28, 18, 18, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155899790 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155899790 Building ZINC001155904748 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155904748 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/968 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1) `ZINC001155904748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155904748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155904748 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 16, 21, 33, 37, 37, 37, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 16, 16, 21, 33, 33, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/969 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1) `ZINC001155904748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155904748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155904748 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 18, 23, 35, 36, 36, 36, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 17, 18, 23, 35, 35, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155904748 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 Building ZINC001155904748 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155904748 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 968) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1) `ZINC001155904748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155904748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155904748 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 11, 16, 21, 33, 37, 37, 37, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 16, 16, 21, 33, 33, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 969) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1) `ZINC001155904748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155904748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155904748 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCC(=O)NC1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 18, 23, 35, 36, 36, 36, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 17, 18, 23, 35, 35, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155904748 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904748 Building ZINC001155904960 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155904960 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/970 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O) `ZINC001155904960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155904960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001155904960 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 18, 29, 45, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 17, 18, 29, 45, 45, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/971 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O) `ZINC001155904960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155904960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001155904960 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 18, 29, 45, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 18, 17, 29, 45, 45, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155904960 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 Building ZINC001155904960 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155904960 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 970) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O) `ZINC001155904960.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155904960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001155904960 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 18, 29, 45, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 17, 18, 29, 45, 45, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 971) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O) `ZINC001155904960.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155904960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001155904960 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCN1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 18, 29, 45, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 18, 17, 29, 45, 45, 47, 47, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155904960 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155904960 Building ZINC001155905102 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905102 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/972 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O) `ZINC001155905102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 16, 28, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 22, 22, 23, 27, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 202 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/973 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O) `ZINC001155905102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 22, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 21, 22, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905102 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 Building ZINC001155905102 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905102 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 972) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O) `ZINC001155905102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905102 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 16, 28, 46, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 22, 22, 23, 27, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 202 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 973) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O) `ZINC001155905102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905102 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 16, 22, 45, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 18, 18, 21, 22, 35, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905102 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905102 Building ZINC001155905103 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905103 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/974 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O) `ZINC001155905103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905103 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 25, 25, 29, 27, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/975 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O) `ZINC001155905103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905103 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 19, 28, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 24, 24, 25, 28, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905103 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 Building ZINC001155905103 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905103 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 974) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O) `ZINC001155905103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905103 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 25, 25, 29, 27, 40, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 975) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O) `ZINC001155905103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155905103 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 19, 28, 47, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 24, 24, 25, 28, 39, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905103 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905103 Building ZINC001155905298 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905298 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/976 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1) `ZINC001155905298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001155905298 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 21, 31, 38, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 20, 20, 31, 38, 38, 38, 38, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/977 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1) `ZINC001155905298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001155905298 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 21, 31, 38, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 20, 20, 31, 38, 38, 38, 38, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905298 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 Building ZINC001155905298 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905298 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 976) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1) `ZINC001155905298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001155905298 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 21, 31, 38, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 20, 20, 31, 38, 38, 38, 38, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 977) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1) `ZINC001155905298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001155905298 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCCn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 13, 21, 31, 38, 38, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 20, 20, 31, 38, 38, 38, 38, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905298 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905298 Building ZINC001155905881 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905881 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/978 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1) `ZINC001155905881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155905881 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 26, 42, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 19, 25, 24, 42, 49, 49, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/979 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1) `ZINC001155905881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155905881 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 25, 40, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 19, 24, 24, 40, 50, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905881 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 Building ZINC001155905881 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155905881 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 978) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1) `ZINC001155905881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155905881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155905881 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 26, 42, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 19, 25, 24, 42, 49, 49, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 364 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 979) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1) `ZINC001155905881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155905881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001155905881 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCNCc1nc(O)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 1, 12, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 15, 25, 40, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 19, 19, 24, 24, 40, 50, 50, 150] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155905881 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155905881 Building ZINC001155906007 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906007 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/980 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O) `ZINC001155906007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906007 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 18, 28, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 24, 24, 25, 28, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/981 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O) `ZINC001155906007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906007 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 17, 28, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 28, 23, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906007 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 Building ZINC001155906007 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906007 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 980) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O) `ZINC001155906007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906007 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 18, 28, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 24, 24, 25, 28, 45, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 981) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O) `ZINC001155906007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906007 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 17, 28, 47, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 23, 23, 28, 23, 43, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906007 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906007 Building ZINC001155906018 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906018 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/982 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O) `ZINC001155906018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906018 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 25, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 25, 23, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/983 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O) `ZINC001155906018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906018 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 29, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 25, 25, 26, 29, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906018 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 Building ZINC001155906018 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906018 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 982) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O) `ZINC001155906018.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906018 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 25, 49, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 21, 25, 23, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 983) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O) `ZINC001155906018.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001155906018 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 18, 29, 48, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 25, 25, 26, 29, 48, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906018 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906018 Building ZINC001155906021 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906021 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/984 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906021 none C[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 48, 32, 19, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 47, 28, 32, 25, 25, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/985 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906021 none C[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 27, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 24, 27, 24, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906021 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 Building ZINC001155906021 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906021 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 984) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906021 none C[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 48, 32, 19, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 48, 48, 48, 47, 28, 32, 25, 25, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 985) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906021 none C[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 27, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 24, 27, 24, 24, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906021 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906021 Building ZINC001155906022 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906022 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/986 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906022 none C[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 28, 20, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 28, 25, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/987 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906022 none C[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 49, 32, 19, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 48, 32, 28, 25, 25, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906022 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 Building ZINC001155906022 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906022 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 986) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906022 none C[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 28, 20, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 28, 25, 25, 25, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 987) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C) `ZINC001155906022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155906022 none C[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1nnnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 49, 32, 19, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 49, 49, 49, 48, 32, 28, 25, 25, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906022 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906022 Building ZINC001155906053 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906053 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/988 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O) `ZINC001155906053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906053 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 19, 18, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/989 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O) `ZINC001155906053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906053 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 23, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 21, 23, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906053 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 Building ZINC001155906053 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906053 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 988) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O) `ZINC001155906053.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906053 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 15, 19, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 17, 17, 19, 18, 28, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 989) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O) `ZINC001155906053.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906053 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 15, 23, 36, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 19, 21, 23, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906053 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906053 Building ZINC001155906054 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906054 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/990 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O) `ZINC001155906054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906054 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 19, 27, 39, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 24, 24, 25, 27, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/991 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O) `ZINC001155906054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906054 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 16, 24, 35, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 23, 24, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906054 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 Building ZINC001155906054 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155906054 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 990) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O) `ZINC001155906054.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155906054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906054 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 19, 27, 39, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 24, 24, 25, 27, 39, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 991) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O) `ZINC001155906054.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155906054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001155906054 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN[C@H]1CCC(=O)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 7, 5, 5, 1, 11, 8, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 16, 24, 35, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 22, 22, 23, 24, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155906054 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155906054 Building ZINC001155913069 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155913069 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/992 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155913069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913069 none CN1CC[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 25, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 25, 23, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/993 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155913069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913069 none CN1CC[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 32, 21, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 32, 29, 28, 28, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155913069 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 Building ZINC001155913069 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155913069 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 992) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155913069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913069 none CN1CC[C@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 25, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 25, 23, 20, 20, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 993) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155913069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913069 none CN1CC[C@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 32, 21, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 32, 29, 28, 28, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155913069 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913069 Building ZINC001155913070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155913070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/994 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155913070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913070 none CN1CC[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 32, 21, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 29, 32, 28, 28, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/995 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155913070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913070 none CN1CC[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 28, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 25, 28, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155913070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 Building ZINC001155913070 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001155913070 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 994) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001155913070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913070 none CN1CC[C@@H](NCCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 32, 21, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 46, 29, 32, 28, 28, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 995) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O) `ZINC001155913070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001155913070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001155913070 none CN1CC[C@@H](NCCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 50, 28, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 25, 28, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001155913070 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001155913070 Building ZINC001156432665 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156432665 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/996 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1cccc(C)c1) `ZINC001156432665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156432665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156432665 none COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 26, 26, 26, 26, 26, 11, 7, 7, 3, 6, 6, 2, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/997 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1) `ZINC001156432665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156432665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156432665 none COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 26, 26, 26, 26, 26, 11, 7, 7, 3, 6, 6, 2, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001156432665 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 Building ZINC001156432665 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156432665 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 996) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1cccc(C)c1) `ZINC001156432665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156432665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156432665 none COC(=O)CNC(=O)CNC(=O)[C@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 26, 26, 26, 26, 26, 11, 7, 7, 3, 6, 6, 2, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 997) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1) `ZINC001156432665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156432665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001156432665 none COC(=O)CNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 7, 11, 3, 3, 1, 3, 1, 1, 1, 6, 6, 2, 6, 6, 6, 26, 26, 26, 26, 26, 11, 7, 7, 3, 6, 6, 2, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001156432665 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156432665 Building ZINC001156597693 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156597693 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/998 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ncon1) `ZINC001156597693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156597693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001156597693 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 15, 34, 34, 34, 34, 15, 15, 15, 10, 10, 2, 6, 6, 6, 6, 6, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/999 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ncon1) `ZINC001156597693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156597693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001156597693 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 16, 41, 41, 41, 41, 16, 16, 16, 9, 9, 2, 6, 6, 6, 6, 6, 41] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001156597693 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 Building ZINC001156597693 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001156597693 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 998) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ncon1) `ZINC001156597693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156597693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001156597693 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 15, 34, 34, 34, 34, 15, 15, 15, 10, 10, 2, 6, 6, 6, 6, 6, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 mkdir: created directory `1' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/1 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 1 (index: 999) grep: /scratch/xiaobo/23902/xdc-8058088.81/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ncon1) `ZINC001156597693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001156597693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001156597693 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 9, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 16, 41, 41, 41, 41, 16, 16, 16, 9, 9, 2, 6, 6, 6, 6, 6, 41] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001156597693 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 1: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/1.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597693 Building ZINC001156597694 mkdir: created directory `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001156597694 mkdir: created directory `0' /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694/0 /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/23902/xdc-8058088.81/working/3D/1000 `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ncon1) `ZINC001156597694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001156597694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001156597694 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ncon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 40, 40, 40, 40, 17, 17, 17, 10, 10, 2, 6, 6, 6, 6, 6, 40] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694 /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Finished preparing ZINC001156597694 Recording results /scratch/xiaobo/23902/xdc-8058088.81/working /scratch/xiaobo/23902/xdc-8058088.81 Appending to /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.* 0: /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694/0.* Removing working files in /scratch/xiaobo/23902/xdc-8058088.81/working/building/ZINC001156597694 /scratch/xiaobo/23902/xdc-8058088.81 Compressing combined databse files /scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/23902/xdc-8058088.81/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/23902/xdc-8058088.81/working/3D/1001' removed directory: `/scratch/xiaobo/23902/xdc-8058088.81/working/3D' rmdir: removing directory, `/scratch/xiaobo/23902/xdc-8058088.81/working/building' rmdir: removing directory, `/scratch/xiaobo/23902/xdc-8058088.81/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/23902/xdc-8058088.81' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdc' `/scratch/xiaobo/23902/xdc-8058088.81/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdc/finished' `/scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xdc/finished/xdc.db2.gz' removed `/scratch/xiaobo/23902/xdc-8058088.81/finished/xdc.db2.gz' removed directory: `/scratch/xiaobo/23902/xdc-8058088.81/finished' removed directory: `/scratch/xiaobo/23902/xdc-8058088.81'